Re: [spctools-discuss] unable to get similar results in TPP 7.1 and earlier versions

[David Shteynberg]

Hello Reeju,

Thank you for trying the TPP for you analysis and for your questions and 
slides.  Here is what I think might be happening.  In 6.3 the scores from comet 
and the PeptideProphet analysis based on the models were different from 7.1.  

Here is the comet f-value model in 6.3:



Here is the f-value model from 7.1:

 


The goal of PeptideProphet is to identify a bimodal distribution and fit two 
distributions to the observed black line, with the corrects modeled in green 
and the incorrect in red.In the first case (6.3) the observed distributions 
is not really bimodal to the eye and the PeptideProphet model is fitting both 
distributions to the one peak because the observed distribution is not bimodal 
enough, and please correct me if I am wrong, you are not providing known true 
negatives (decoys) to help train the model and keep the red distribution 
“pinned" by them.  In the second case (7.1), the bimodal distribution is 
fitting much better in my opinion as the red curve is mostly in the correct 
place and the green model is fitting the shoulder where the majority of the 
correct PSMs in your data will be.   I know you feel like you “lost” some IDs 
going fro m 6.3 analysis to 7.1, but I would say you likely improved the 
confidence in the results by the reanalysis.  You can verify this by 
incorporating unknown true negatives (entrapement decoys) in you database to 
use as another FDR estimate to compare to the model’s results from 6.3 and 7.1.


Cheers!
-David

> On Sep 2, 2024, at 5:44 AM, reeju  wrote:
> 
> Hello everyone,
> I am running a raw file in TPP 7.1, which was also analyzed previously in an 
> earlier version via TPP 6.3. I have kept the comet parameters and peptide 
> prophet settings similar for both the cases, still there is difference in 
> proteins identified from both TPP versions. In tpp6.3 the total proteins 
> identified were 1546, after applying filters on the same file with 
> probability 0.88(having 0.05 error rate) the protein count was still 494. But 
> in tpp 7.1 the total protein count displayed was only 99 without any 
> filtering on the same file. Why is there such a drastic difference. 
> Comparison of both files have been attached. If anyone can help us 
> troubleshoot please revert back.
> Thank You
> Regards
> 
> 
> --
> Reeju Rani
> Research Scholar
> Proteomics and Cell Biology lab
> ICAR-National Dairy Research Institute
> Karnal, Haryana India
> 
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>  
> .
> 

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Re: [spctools-discuss] Issues with processing .d (Bruker) files run in DDA-LFQ mode

['David Shteynberg' via spctools-discuss]

Hello Shagun,

I think there is nothing specific in the TPP that makes it more or less
suited for a particular instrument, manufacturer or experimental setup,
however, it is important to give the tools good parameters to expect good
results, assuming good data.

As far as new features in the TPP 7.0.0 (and beyond,)  StPeter label-free
quantitation that computes spectral indices has new features in TPP 7 that
allow it to separate the protein quantities in one ProteinProphet resulting
protXML file, "by run" or "by experiment" which helps the user compare
protein quantities across runs or across experiments.  We hope this is
useful.

Cheers!

-David

On Thu, Aug 15, 2024 at 10:34 AM Shagun Gupta  wrote:

> Hi David
>
> Thank you for your prompt response. I’ll try out your suggestions today
> and will update you on the results or if I encounter any issues.
>
> Quick question—are there any specific features in the latest version of
> TPP that make it particularly well-suited for DDA-LFQ analysis on Bruker
> instruments?
>
> Best
> Shagun
>
> On Wednesday, August 14, 2024 at 11:47:31 AM UTC-4 David Shteynberg wrote:
>
>> Hello Shagun,
>>
>> I was able to run comet and the TPP on these files from the latest TPP
>> version 7.1.0.  After adding two independent deBruijn randomized decoys to
>> the database using the Petunia Decoy Database tool, my pipeline found
>> approximately 80 thousand to almost 90 thousand PSMs at 1% spectrum error
>> rate, per mzML file.  These map to about 68 thousand unique peptides at 1%
>> peptide error rate, after iProphet combining all the files.  ProteinProphet
>> mapped all of these to just over 7000 proteins at 1% protein error rate (or
>> lower.)
>>
>> The biggest issue I found in your comet params file was the was
>> n-terminal acetylation was specified using MSFragger notation ‘[^’ for the
>> amino acid (should be ’n’ instead for comet.)  Unfortunately this confused
>> the pipeline and exposed downstream assumptions that broke the analysis.
>>
>> I am attaching the comet params file I used to process this data.
>>
>> Cheers!
>> -David
>>
>> P.S.  Please update your TPP to the latest 7.1.0 to get the latest
>> features and bug-fixes!
>>
>> --
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> .
>

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Re: [spctools-discuss] Issues with processing .d (Bruker) files run in DDA-LFQ mode

[David Shteynberg]

Hello Shagun,I was able to run comet and the TPP on these files from the latest TPP version 7.1.0.  After adding two independent deBruijn randomized decoys to the database using the Petunia Decoy Database tool, my pipeline found approximately 80 thousand to almost 90 thousand PSMs at 1% spectrum error rate, per mzML file.  These map to about 68 thousand unique peptides at 1% peptide error rate, after iProphet combining all the files.  ProteinProphet mapped all of these to just over 7000 proteins at 1% protein error rate (or lower.)The biggest issue I found in your comet params file was the was n-terminal acetylation was specified using MSFragger notation ‘[^’ for the amino acid (should be ’n’ instead for comet.)  Unfortunately this confused the pipeline and exposed downstream assumptions that broke the analysis. I am attaching the comet params file I used to process this data.  Cheers!-DavidP.S.  Please update your TPP to the latest 7.1.0 to get the latest features and bug-fixes!



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ShagunGupta.comet.params
Description: Binary data
On Aug 13, 2024, at 2:15 PM, Shagun Gupta  wrote:Hi DavidApologies for the hassle! I have uploaded the .d files in an unzipped format under TPP_diagnosis/TPP_diagnosis. Let me know if this works instead?BestShagunOn Tuesday, August 13, 2024 at 3:09:37 PM UTC-4 David Shteynberg wrote:Hello Shagun,I downloaded the larger zip file twice and tried to decompress, but each time it told me there was a corruption in the zip file.  The smaller files downloaded fine.  Can you check your file and upload again?Thanks!-DavidOn Tue, Aug 13, 2024 at 9:47 AM Shagun Gupta <sg2...@cornell.edu> wrote:Hi DavidI have attached a link to the following files - one replicate per condition .d file (file starting with "C_" had IDs but no values that could be extracted for quantification)- comet parameter file I used- fasta file I ran the search with.Let me know if I can share anything else!Box_link_diagnosisBestShagunOn Tuesday, August 13, 2024 at 11:05:42 AM UTC-4 David Shteynberg wrote:Hello Shagun,Thank you for the detailed report.  If you are able, please first compress (into a zip or similar) and then share some of the problem .d files so I can try to replicate this issue on my computer before I offer any suggestions.  Cheers!-DavidOn Tue, Aug 13, 2024 at 7:50 AM Shagun Gupta <sg2...@cornell.edu> wrote:Hi allI have been experiencing issues processing .d files obtained from a Bruker timsTOF HT in DDA-LFQ mode, more specifically getting quantification - precursor intensity - per spectra. I am using TPP V6.3.3 Arcus on a windows computer. Details- There are 12 .d files (4 repeats of 3 conditions) composed of a human with yeast proteome spike in at different ratios.- Converted to .mzXML using msconvert- Searched with COMET and a search database taken from UniProt for Homo sapiens+Yeast- Processed with PeptideProphet (filtered at probability associated with 1% FDR), XPRESS, ProteinProphet. Ran with -PREC flag (PeptideProphet), -i flag (XPRESS)- Want to do hypothesis testing (comparing the three conditions pairwise) using MSstats. So require raw precursor intensity values to make a file that can be used as input to MSstats.Unfortunately after trying the above, and a few more things, while I get a large number of PSMs passing FDR (~30k), a large proportion of them do not have any precursor intensity value (<1k have some "light area" values). Using the "light area" values also does not give expected results (its a benchmarking dataset and processing with MSFragger gave excellent results that align with expected ratios etc.). Could you suggest things I could be doing differently to get the right results? (I imagine it might have something to do with the initial conversion to mzXML itself?) Happy to share any other details needed!BestShagun

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Re: [spctools-discuss] Issues with processing .d (Bruker) files run in DDA-LFQ mode

['David Shteynberg' via spctools-discuss]

Hello Shagun,

Thank you!  I was able to download your data this time and convert it to
mzML files.
Internally, we use tdf2mzml.py to convert the .d directories into mzML
files for the TPP for DIA data, (diapysef for DDA data.)   Here is an
example of the command we use on our linux computer:


tdf2mzml.py --ms1_type centroid --compression zlib -i
A_500ng_DDA_HM10_100_1p9_25minGT_Slot2-1_1_4647.d -o
A_500ng_DDA_HM10_100_1p9_25minGT_Slot2-1_1_4647.mzML

Would you be willing to try using that converter to generate the mzML files
before you search with Comet+TPP?

Thanks!
-David

On Tue, Aug 13, 2024 at 2:16 PM Shagun Gupta  wrote:

> Hi David
>
> Apologies for the hassle! I have uploaded the .d files in an unzipped
> format under TPP_diagnosis/TPP_diagnosis. Let me know if this works instead?
>
> Best
> Shagun
>
> On Tuesday, August 13, 2024 at 3:09:37 PM UTC-4 David Shteynberg wrote:
>
>> Hello Shagun,
>>
>> I downloaded the larger zip file twice and tried to decompress, but each
>> time it told me there was a corruption in the zip file.  The smaller files
>> downloaded fine.  Can you check your file and upload again?
>>
>> Thanks!
>> -David
>>
>> On Tue, Aug 13, 2024 at 9:47 AM Shagun Gupta  wrote:
>>
>>> Hi David
>>>
>>> I have attached a link to the following files
>>> - one replicate per condition .d file (file starting with "C_" had IDs
>>> but no values that could be extracted for quantification)
>>> - comet parameter file I used
>>> - fasta file I ran the search with.
>>>
>>> Let me know if I can share anything else!
>>>
>>> Box_link_diagnosis
>>> <https://cornell.box.com/s/5y2uak2twszajaniaqpnevxn4zdneu54>
>>> Best
>>> Shagun
>>>
>>> On Tuesday, August 13, 2024 at 11:05:42 AM UTC-4 David Shteynberg wrote:
>>>
>>>> Hello Shagun,
>>>>
>>>> Thank you for the detailed report.  If you are able, please first
>>>> compress (into a zip or similar) and then share some of the problem .d
>>>> files so I can try to replicate this issue on my computer before I offer
>>>> any suggestions.
>>>>
>>>> Cheers!
>>>> -David
>>>>
>>>> On Tue, Aug 13, 2024 at 7:50 AM Shagun Gupta 
>>>> wrote:
>>>>
>>>>> Hi all
>>>>>
>>>>> I have been experiencing issues processing .d files obtained from a
>>>>> Bruker timsTOF HT in DDA-LFQ mode, more specifically getting 
>>>>> quantification
>>>>> - precursor intensity - per spectra. I am using TPP V6.3.3 Arcus on a
>>>>> windows computer.
>>>>>
>>>>> Details
>>>>> - There are 12 .d files (4 repeats of 3 conditions) composed of a
>>>>> human with yeast proteome spike in at different ratios.
>>>>> - Converted to .mzXML using msconvert
>>>>> - Searched with COMET and a search database taken from UniProt for
>>>>> Homo sapiens+Yeast
>>>>> - Processed with PeptideProphet (filtered at probability associated
>>>>> with 1% FDR), XPRESS, ProteinProphet. Ran with -PREC flag 
>>>>> (PeptideProphet),
>>>>> -i flag (XPRESS)
>>>>> - Want to do hypothesis testing (comparing the three conditions
>>>>> pairwise) using MSstats. So require raw precursor intensity values to make
>>>>> a file that can be used as input to MSstats.
>>>>>
>>>>> Unfortunately after trying the above, and a few more things, while I
>>>>> get a large number of PSMs passing FDR (~30k), a large proportion of them
>>>>> do not have any precursor intensity value (<1k have some "light area"
>>>>> values). Using the "light area" values also does not give expected results
>>>>> (its a benchmarking dataset and processing with MSFragger gave excellent
>>>>> results that align with expected ratios etc.). Could you suggest things I
>>>>> could be doing differently to get the right results? (I imagine it might
>>>>> have something to do with the initial conversion to mzXML itself?)
>>>>>
>>>>> Happy to share any other details needed!
>>>>>
>>>>> Best
>>>>> Shagun
>>>>>
>>>>> --
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>>>>> To unsub

Re: [spctools-discuss] Issues with processing .d (Bruker) files run in DDA-LFQ mode

['David Shteynberg' via spctools-discuss]

Hello Shagun,

I downloaded the larger zip file twice and tried to decompress, but each
time it told me there was a corruption in the zip file.  The smaller files
downloaded fine.  Can you check your file and upload again?

Thanks!
-David

On Tue, Aug 13, 2024 at 9:47 AM Shagun Gupta  wrote:

> Hi David
>
> I have attached a link to the following files
> - one replicate per condition .d file (file starting with "C_" had IDs but
> no values that could be extracted for quantification)
> - comet parameter file I used
> - fasta file I ran the search with.
>
> Let me know if I can share anything else!
>
> Box_link_diagnosis
> <https://cornell.box.com/s/5y2uak2twszajaniaqpnevxn4zdneu54>
> Best
> Shagun
>
> On Tuesday, August 13, 2024 at 11:05:42 AM UTC-4 David Shteynberg wrote:
>
>> Hello Shagun,
>>
>> Thank you for the detailed report.  If you are able, please first
>> compress (into a zip or similar) and then share some of the problem .d
>> files so I can try to replicate this issue on my computer before I offer
>> any suggestions.
>>
>> Cheers!
>> -David
>>
>> On Tue, Aug 13, 2024 at 7:50 AM Shagun Gupta  wrote:
>>
>>> Hi all
>>>
>>> I have been experiencing issues processing .d files obtained from a
>>> Bruker timsTOF HT in DDA-LFQ mode, more specifically getting quantification
>>> - precursor intensity - per spectra. I am using TPP V6.3.3 Arcus on a
>>> windows computer.
>>>
>>> Details
>>> - There are 12 .d files (4 repeats of 3 conditions) composed of a human
>>> with yeast proteome spike in at different ratios.
>>> - Converted to .mzXML using msconvert
>>> - Searched with COMET and a search database taken from UniProt for Homo
>>> sapiens+Yeast
>>> - Processed with PeptideProphet (filtered at probability associated with
>>> 1% FDR), XPRESS, ProteinProphet. Ran with -PREC flag (PeptideProphet), -i
>>> flag (XPRESS)
>>> - Want to do hypothesis testing (comparing the three conditions
>>> pairwise) using MSstats. So require raw precursor intensity values to make
>>> a file that can be used as input to MSstats.
>>>
>>> Unfortunately after trying the above, and a few more things, while I get
>>> a large number of PSMs passing FDR (~30k), a large proportion of them do
>>> not have any precursor intensity value (<1k have some "light area" values).
>>> Using the "light area" values also does not give expected results (its a
>>> benchmarking dataset and processing with MSFragger gave excellent results
>>> that align with expected ratios etc.). Could you suggest things I could be
>>> doing differently to get the right results? (I imagine it might have
>>> something to do with the initial conversion to mzXML itself?)
>>>
>>> Happy to share any other details needed!
>>>
>>> Best
>>> Shagun
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/cf666974-5c1f-4de0-80ad-d9b1df2173dan%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/cf666974-5c1f-4de0-80ad-d9b1df2173dan%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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>

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Re: [spctools-discuss] Issues with processing .d (Bruker) files run in DDA-LFQ mode

['David Shteynberg' via spctools-discuss]

Hello Shagun,

Thank you for the detailed report.  If you are able, please first compress
(into a zip or similar) and then share some of the problem .d files so I
can try to replicate this issue on my computer before I offer any
suggestions.

Cheers!
-David

On Tue, Aug 13, 2024 at 7:50 AM Shagun Gupta  wrote:

> Hi all
>
> I have been experiencing issues processing .d files obtained from a Bruker
> timsTOF HT in DDA-LFQ mode, more specifically getting quantification -
> precursor intensity - per spectra. I am using TPP V6.3.3 Arcus on a windows
> computer.
>
> Details
> - There are 12 .d files (4 repeats of 3 conditions) composed of a human
> with yeast proteome spike in at different ratios.
> - Converted to .mzXML using msconvert
> - Searched with COMET and a search database taken from UniProt for Homo
> sapiens+Yeast
> - Processed with PeptideProphet (filtered at probability associated with
> 1% FDR), XPRESS, ProteinProphet. Ran with -PREC flag (PeptideProphet), -i
> flag (XPRESS)
> - Want to do hypothesis testing (comparing the three conditions pairwise)
> using MSstats. So require raw precursor intensity values to make a file
> that can be used as input to MSstats.
>
> Unfortunately after trying the above, and a few more things, while I get a
> large number of PSMs passing FDR (~30k), a large proportion of them do not
> have any precursor intensity value (<1k have some "light area" values).
> Using the "light area" values also does not give expected results (its a
> benchmarking dataset and processing with MSFragger gave excellent results
> that align with expected ratios etc.). Could you suggest things I could be
> doing differently to get the right results? (I imagine it might have
> something to do with the initial conversion to mzXML itself?)
>
> Happy to share any other details needed!
>
> Best
> Shagun
>
> --
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> 
> .
>

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Re: [spctools-discuss] converting prot.xml to tsv file error

['David Shteynberg' via spctools-discuss]

Thank you for confirming!

On Mon, Aug 5, 2024, 11:37 AM Karla Joanna Rojas Mendez <
karla.ro...@ibt.unam.mx> wrote:

> Hello David,
>
> The file fixed the problem, thanks for your help.
>
> Cheers.
>
>
>
> El viernes, 2 de agosto de 2024 a la(s) 10:53:56 a.m. UTC-6, David
> Shteynberg escribió:
>
>> Hello Karla,
>>
>> Please find the file of *ProtXMLViewer.pl* in your TPP installation
>> directory, *C:/TPP/cgi-bin/ ,*and make a copy of this file for a backup,
>> just in case.  Next, place the patched file attached to this message in the
>> same directory.  This should fix the export of StPeter value using the
>> ProtXMLViewer.pl web interface.  Keep us posted to your progress.
>>
>> Cheers!
>> -David
>>
>>
>>
>> On Fri, Aug 2, 2024 at 9:04 AM Karla Joanna Rojas Mendez <
>> karla...@ibt.unam.mx> wrote:
>>
>>> Hello,
>>>
>>> I am using windows 11.
>>>
>>> thanks for your help
>>>
>>> El martes, 30 de julio de 2024 a la(s) 4:39:53 p.m. UTC-6, David
>>> Shteynberg escribió:
>>>
>>>> Hello Karla,
>>>>
>>>> Thanks to your bug report I was able to track down and correct an issue
>>>> with tsv export from the ProtXMLViewer page.  This change will be made in
>>>> the next release.  Meanwhile, if you can tell me the operating system where
>>>> you are using the TPP I would be happy to send you an appropriate patch for
>>>> testing.
>>>>
>>>> Cheers!
>>>> -David
>>>>
>>>> On Jul 30, 2024, at 11:08 AM, Karla Joanna Rojas Mendez <
>>>> karla...@ibt.unam.mx> wrote:
>>>>
>>>> Hi,
>>>> when I convert the file interact.ipro.prot.xml to tsv the information
>>>> in the .tsv file is incomplete the sln and ng information is empty an the
>>>> number of proteins in the file it is also incomplete.
>>>>
>>>> I don´t use any filter on the files, i convert them from the file that
>>>> comes directly from the analysis.
>>>>
>>>>  How can I fix this?
>>>>
>>>> Thank you
>>>>
>>>> >>> 2024-07-30 115504.png>
>>>>
>>>>
>>>> --
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>>>> Groups "spctools-discuss" group.
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>>>> an email to spctools-discu...@googlegroups.com.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/spctools-discuss/3e4ceccd-5d5b-4097-87e2-c63293dddaf7n%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/spctools-discuss/3e4ceccd-5d5b-4097-87e2-c63293dddaf7n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>> >>> 2024-07-30 115504.png>
>>>>
>>>>
>>>> --
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>>> <https://groups.google.com/d/msgid/spctools-discuss/d922f009-6700-44a5-8a87-4fdaa6ed13ban%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
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Re: [spctools-discuss] Can anyone share notepad version of comet.param version 2024

[David Shteynberg]

It sounds like you are most interested in the identified peptides rather than 
the sufficient set of proteins able to explain all of your peptide 
observations.  The peptides you are seeing map to many proteins, and 
unfortunately you are not observing peptides that would individually 
distinguish the protein isoforms.  Unfortunately, this is likely a common 
problem and there is no one size fits all solution.  Maybe the search 
parameters tolerances and PTMs can be further optimized? Perhaps the isoforms 
you are seeking are modified with some PTM that is currently not in your 
parameter set?  Maybe you can apply a targeted acquisition, going specifically 
after the peptides that would distinguish the isoforms?  Not really sure, but 
the TPP data-driven analysis seems to be working ok in providing some clues, 
given the data.  

Cheers!
-David 

> On Aug 1, 2024, at 3:30 AM, sudarshan kumar  wrote:
> 
> Hi David 
> thank you so much. I learnt a lot from your discussion.
> 
> Can you please go through the ppt? I have questions regarding how to include 
> 0 probability assigned isoform of a protein in our list of identified 
> protein. It is not possible if  i use the error rate cutoff criteria to sort 
> the list. 
> Case- I am studying tissue proteome. It has more than 30 isoforms of a 
> protein called pregnancy associated glycoprotein. I miss many of them in my 
> list of protiens if i filter the protiens list as per the error rate of .05
> 
> sensitivity: error table gives me the last error rate cutoff of .2086. How 
> advisable is it to move down still lower like .1 or .01.
> 
> When I lower the min_prob cutoff beyond .2086, it increases the number of 
> identification by including more proteins which belong to the already 
> reported "group of protein" some of which are with high number of PSM. I can 
> see those isoforms also. 
> 
> Please give your expert opinion. 
> 
> 
> 
> 
> 
> 
> 
> On Wed, Jul 31, 2024 at 9:27 AM 'David Shteynberg' via spctools-discuss 
>  <mailto:spctools-discuss@googlegroups.com>> wrote:
>> Absolutely!  Another thing to understand here is that the statistical 
>> analysis happens on several data reduction layers where PeptideProphet works 
>> on the level of PSMs, iProphet works of the level of peptide sequences and 
>> ProteinProphet works on the level of proteins.  Since these layers stack on 
>> top of each other, small errors from incorrect statistics at an earlier 
>> layer propagate into much larger errors at the lower levels.  Keeping 
>> entrapment decoys in the database allows one to have another evaluation of 
>> the error in addition to the TPP models' estimation and provides an FDR 
>> estimate that is independent from the TPP.  Unlike "True Positives", 
>> independent entrapment decoys are "True Negative" random matches that are 
>> not biased by the researcher's prior expectations.  
>> 
>> Also, there maybe a misunderstanding: as you lower the minimum probability 
>> threshold the error increases, and the sensitivity also increases (hopefully 
>> much faster than the error!)
>> 
>> Cheers!
>> 
>> -David
>> 
>> On Wed, Jul 31, 2024, 1:02 AM sudarshan kumar > <mailto:kumarsuders...@gmail.com>> wrote:
>>> Hi David,
>>> I am reading your paragraph again and again to understand it fully and word 
>>> by word
>>> 
>>> You said -  I recommend you focus on the sensitivity of your analysis 
>>> rather than the absolute total of proteins identified, without 
>>> consideration for error
>>> 
>>> I usually take the 0.05 error to use the minimum probability cutoff to sort 
>>> my data. You mean to suggest me that I can go for higher sensitivity. If I 
>>> see this table - at higher sensitivity also (.8965) I am getting similar 
>>> (5268) number of correct hits which correspondence to the error rate of 
>>> .02. Even if i am increasing the sensitivity threshold on my data- the 
>>> correct hits keeps going down (as per the statistics) which will further 
>>> reduce the absolute number of correct proteins identified. 
>>> 
>>> As a researcher I want only the least number of the spectra should be 
>>> discarded by the prophet. What intrigues me is that - out of 88000 
>>> scans/spectra only 5000 are assigned to peptides at an error rate of .05. 
>>> Do you think this is normal?
>>> 
>>> 
>>> 
>>> On Tue, Jul 30, 2024 at 7:54 AM David Shteynberg 
>>> mailto:dshteynb...@systemsbiology.org>> 
>>> wrote:
>>>> Hello Sud,
>>>

Re: [spctools-discuss] converting prot.xml to tsv file error

[David Shteynberg]

Hello Karla,

Thanks to your bug report I was able to track down and correct an issue with 
tsv export from the ProtXMLViewer page.  This change will be made in the next 
release.  Meanwhile, if you can tell me the operating system where you are 
using the TPP I would be happy to send you an appropriate patch for testing.

Cheers!
-David

> On Jul 30, 2024, at 11:08 AM, Karla Joanna Rojas Mendez 
>  wrote:
> 
> Hi,
> when I convert the file interact.ipro.prot.xml to tsv the information in the 
> .tsv file is incomplete the sln and ng information is empty an the number of 
> proteins in the file it is also incomplete.
> 
> I don´t use any filter on the files, i convert them from the file that comes 
> directly from the analysis.
> 
>  How can I fix this?
> 
> Thank you
>  115504.png>
> 
> 
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>  
> .
>  115504.png>

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Re: [spctools-discuss] Can anyone share notepad version of comet.param version 2024

[David Shteynberg]

Hello Sud,

Please remember the job of the TPP is to separate the correct results (signal) 
from the random matches (noise) on the PSM level, peptide level (PTM-level) and 
protein level.  Generally speaking most datasets have a large portion of 
incorrect PSMs, which by the nature of statistics will match to random peptides 
and proteins selected from the search database.  It is standard in our lab that 
we see large analysis of tens of millions of correct PSMs that map to tens of 
thousands of the correct peptides and perhaps only a few thousand or so 
proteins, depending on the sample (e.g. blood plasma.). So I am not concerned 
about the total numbers of proteins you are seeing after applying statistical 
cut-offs.  Certainly there are other models you can try in PeptideProphet that 
might alter your results slightly.  To have a deeper look at your data you have 
to find where the other correct PSMs might be recovered, e.g. you can try a 
semi-tryptic (or unconstrained) search, as we did in this thread, if you think 
the digestion was the issue.  Also, you can search for additional PTMs that are 
present in the sample but the existing search is missing.  I recommend you 
focus on the sensitivity of your analysis rather than the absolute total of 
proteins identified, without consideration for error. The goal of these tools 
is to give you a user-controlled accurate error rate while maximizing the 
sensitivity (number of correct identifications out of the total correct 
identifications possible in the entire analysis.).   One way to apply the TPP 
is to use the results to improve the laboratory methods to try maximize the 
return of correct proteins from the samples.  Also replicates, biological and 
technical are very helpful to help separate the correct signal from random 
noise.

Hope this helps!

-David

> On Jul 30, 2024, at 5:52 AM, sudarshan kumar  wrote:
> 
> Hi David,
> Thank you for clearing my doubts. 
> 
> I have few more queries -
> you said "The reason you are seeing many more protein numbers in the PepXML 
> Viewer (Summary Tab) as opposed to after running ProteinProphet is likely 
> because you haven’t applied any threshold filtering to the probability (or 
> other scores). You are seeing all the hits here as opposed to the “likely 
> correct” hits."
> 
> I tried to anlayze other run files. It is a blood sample run on orbitrap 
> fusion. The total number of scans are around 88000 (I consider it a high 
> number).
> till comet search there are many peptides hits (upto 5). But as soon as I 
> put stats/models of validation (peptide prophet or iprophet) the number of 
> unique peptides falls down to 300. This drastic reduction in the number of 
> accurate peptides and hence proteins as well force me to think that I am not 
> using correct statistiical models.
> 
> I assume that from such a large number of PSM getting only 300 proteins that 
> too iin blood, is unbelievable. 
> 
> 
> original without puttin error filter
> 
> 
> 
> 
> 
> 
> 
> On Mon, Jul 29, 2024 at 8:02 AM David Shteynberg 
> mailto:dshteynb...@systemsbiology.org>> 
> wrote:
>> Hello Sud,
>> 
>> No problem!
>> 
>> There is a difference between when PeptideProphet reports a probability of 
>> “0” for a PSM vs a probability of “0.”.   The lone zero “0” is used to 
>> represent the case when PeptideProphet model did not find a successful model 
>> for a mixture distribution of correct and incorrect result and returned no 
>> model as opposed to the model gave a low probability.  So, if all your 
>> probabilities come back as “0” it means no model and you have to either 
>> adjust analysis model or search parameters or look for another issue with 
>> the data, when you see “0.” it means the spectrum had a low score based 
>> on the model that was returned.
>> 
>> The reason you are seeing many more protein numbers in the PepXML Viewer 
>> (Summary Tab) as opposed to after running ProteinProphet is likely because 
>> you haven’t applied any threshold filtering to the probability (or other 
>> scores). You are seeing all the hits here as opposed to the “likely correct” 
>> hits.
>> 
>> Regarding the Butyrophilin, it appears to have several isoforms of which the 
>> first one that got the high probability is necessary to explain all the 
>> observed peptides for this isoform protein family group, the other proteins 
>> in the family share many of the peptides with the tops hit, and come along 
>> for the ride, without having independent peptide evidence that would 
>> distinguish them from the other isoforms.
>> 
>> Please let me know when you have further questions.
>> 
>> Cheers!
>> -David 
>> 
>>

Re: [spctools-discuss] Can anyone share notepad version of comet.param version 2024

[David Shteynberg]

Hello Sud,

No problem!

There is a difference between when PeptideProphet reports a probability of “0” 
for a PSM vs a probability of “0.”.   The lone zero “0” is used to 
represent the case when PeptideProphet model did not find a successful model 
for a mixture distribution of correct and incorrect result and returned no 
model as opposed to the model gave a low probability.  So, if all your 
probabilities come back as “0” it means no model and you have to either adjust 
analysis model or search parameters or look for another issue with the data, 
when you see “0.” it means the spectrum had a low score based on the model 
that was returned.

The reason you are seeing many more protein numbers in the PepXML Viewer 
(Summary Tab) as opposed to after running ProteinProphet is likely because you 
haven’t applied any threshold filtering to the probability (or other scores). 
You are seeing all the hits here as opposed to the “likely correct” hits.

Regarding the Butyrophilin, it appears to have several isoforms of which the 
first one that got the high probability is necessary to explain all the 
observed peptides for this isoform protein family group, the other proteins in 
the family share many of the peptides with the tops hit, and come along for the 
ride, without having independent peptide evidence that would distinguish them 
from the other isoforms.

Please let me know when you have further questions.

Cheers!
-David 


> On Jul 29, 2024, at 4:55 AM, sudarshan kumar  wrote:
> 
> Hi David,
> Thank you so much for doing an exhaustive study on the data. 
> Yes I agree with your keen observation that the data seems more kind of 
> poorly digested peptides. I repeated the analysis with both semi as well as 
> fully. I was getting 0 probability for fully digested searched data from 
> comet (though in comet search there were correct hits). While in semi tryptic 
> search (both peptide prophet and iprophet) returned proteins with good 
> probability. 
> I wonder-  in the summary tab I see there are proteins identified to the tune 
> of around 300 but when I look at the protein detail sheet (sorted by PSM 
> number) it shows hardly 10-12 proteins with at least 1 PSM. Rest all entries 
> are with 0 PSM. Why this? Please explain to me. Can you please also explain - 
> when i see the top hit (as per the number of highest PSM), there are more 
> than 150 PSM for it. While the list of identified proteins (with at least one 
> PSM) is very small - hardly 10-12. Why? Though I expected more number of hits 
> with evenly distributed PSM number across the proteins. 
> 
> Thank you so much!
> 
> 
> 
> On Sat, Jul 27, 2024 at 4:13 AM David Shteynberg 
> mailto:dshteynb...@systemsbiology.org>> 
> wrote:
>> Hello again Sud,
>> 
>> -- 
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>> email to spctools-discuss+unsubscr...@googlegroups.com 
>> <mailto:spctools-discuss+unsubscr...@googlegroups.com>.
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>> https://groups.google.com/d/msgid/spctools-discuss/E48C9F54-97ED-4825-AA14-CF84A8956729%40systemsbiology.org
>>  
>> <https://groups.google.com/d/msgid/spctools-discuss/E48C9F54-97ED-4825-AA14-CF84A8956729%40systemsbiology.org?utm_medium=email&utm_source=footer>.
>> 
>> First, you can find my comet.params file attached.  It is modified to a set 
>> of parameters that I selected after having played a bit more with your 
>> dataset to try to discover some other reason why you might be getting low 
>> number of correct IDs.  One thing I am noticing (after having performed a 
>> semi-tryptic search with comet) is that the majority of correct peptide IDs 
>> are semi-tryptic.  This is expected among incorrect results, but among 
>> correct results this indicates a potential issue with tryptic digestion of 
>> the sample.  The model for NTT is learned automatically by PeptideProphet 
>> and is pasted here:
>> 
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>>  
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Re: [spctools-discuss] Peptide prophet showing all zero probability

['David Shteynberg' via spctools-discuss]

also required are your search params and db

On Thu, Jul 25, 2024, 5:14 AM sudarshan kumar 
wrote:

>  20240417_AN_171_POS_LCMSMS_00.shrunken.mzML
> <https://drive.google.com/file/d/16xvJYrOzHzb0jjXse-XY50gHGs7YGJFW/view?usp=drive_web>
>
>
> On Tue, Jul 23, 2024 at 10:16 AM David Shteynberg <
> dshteynb...@systemsbiology.org> wrote:
>
>> Hello Sudarshan,
>>
>> Although it is not possible to tell exactly what happened here without
>> more information, the usual suspects are:
>>
>> 1.  Data Quality
>> 2.  Incorrect Database
>> 3.  Incorrect Parameters
>>
>> I just ran a test of X!Tandem locally on the ISB18 dataset.  The search
>> ran and the TPP validation generated PSMs with positive probability
>> values.  If you are able to provide more information about your specific
>> analysis or post your dataset online for download I would be happy to take
>> a closer look.
>>
>> Cheers!
>> -David
>>
>>
>>
>>
>> On Jul 23, 2024, at 4:56 AM, sudarshan kumar 
>> wrote:
>>
>> Hi,
>> Can you please explain why?
>> When I searched with tandem, IT shows all good hits as I expected from
>> the sample.
>> But when I used peptide prophet, The result is all 0 probability?
>> I tried merging 4 files and individually also. But in all cases the
>> probability comes to 0.
>>
>> where is the problem>
>>
>> Best
>>
>> --
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>> .
>>
>>
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>> .
>>
>
>
> --
> ---
> The real voyage of discovery consists not in seeking new lands but seeing
> with new eyes. — Marcel Proust
>
> Dr. Sudarshan Kumar
> (Fulbright-Nehru Fellow)
> (B.V.Sc.& A.H., M.V.Sc., PhD.)
> Sr. Scientist
> Animal Biotechnology Center
> (Proteomics and Cell Biology Lab.)
> National Dairy Research Institute Karnal, 132001
> Haryana, India
> Contact No 09254912456
> URL www.ndri.res.in
> Orcid Id: https://orcid.org/-0002-9816-4307
>
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> .
>

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Re: [spctools-discuss] SWATH analysis

[David Shteynberg]

The TPP has tools for extracting searchable fragments from DIA data that can be 
searched like any other DDA data.  The tool is called DISCo and there is a 
tutorial available here:

http://www.tppms.org/tutorials/

Among the tutorials we offer you should be able to find “DIA Analysis.”  Please 
report back with any questions, problems or accolades ;).

Cheers!
-David


> On Jul 24, 2024, at 1:14 AM, dr.gunj...@gmail.com  
> wrote:
> 
> I am new to TPP. Is it possible to use TPP for SWATH data analysis?
> If yes, could you please help with the workflow (step by step)
> 
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>  
> .

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Re: [spctools-discuss] Peptide prophet showing all zero probability

[David Shteynberg]

Hello again Sud!

>From your screen shots I could tell you are running version 6.3.2 of the 
>software.  I think the issue you are seeing might be a solved one in the 
>latest release 7.1.0.  Are you able to update and try the latest version?

Thanks!
-David

> On Jul 24, 2024, at 7:38 AM, David Shteynberg 
>  wrote:
> 
> Can you compress the mzML file, the search database and your search together 
> and reshare?  I will need at least those file to try to reproduce your 
> process.
> 
> Cheers!
> 
> On Wed, Jul 24, 2024, 2:19 AM sudarshan kumar  <mailto:kumarsuders...@gmail.com>> wrote:
>> 
>>  20240417_AN_171_POS_LCMSMS_00.mzML 
>> <https://drive.google.com/file/d/1qNf8C08bcg0KwF56HmonihILxh3uVqyU/view?usp=drive_web>please
>>  find the mzml file shared through drive
>> 
>> On Wed, Jul 24, 2024 at 12:40 AM sudarshan kumar > <mailto:kumarsuders...@gmail.com>> wrote:
>>> Thank you so much  David,
>>> Please find the screenshot of what I am getting. 
>>> I am sharing the file also for you to check please.
>>> Best regards,
>>> Sud
>>> 
>>> 
>>> On Tue, Jul 23, 2024 at 10:16 AM David Shteynberg 
>>> mailto:dshteynb...@systemsbiology.org>> 
>>> wrote:
>>>> Hello Sudarshan,
>>>> 
>>>> Although it is not possible to tell exactly what happened here without 
>>>> more information, the usual suspects are:
>>>> 
>>>> 1.  Data Quality
>>>> 2.  Incorrect Database
>>>> 3.  Incorrect Parameters
>>>> 
>>>> I just ran a test of X!Tandem locally on the ISB18 dataset.  The search 
>>>> ran and the TPP validation generated PSMs with positive probability 
>>>> values.  If you are able to provide more information about your specific 
>>>> analysis or post your dataset online for download I would be happy to take 
>>>> a closer look.
>>>> 
>>>> Cheers!
>>>> -David
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On Jul 23, 2024, at 4:56 AM, sudarshan kumar >>>> <mailto:kumarsuders...@gmail.com>> wrote:
>>>>> 
>>>>> Hi, 
>>>>> Can you please explain why?
>>>>> When I searched with tandem, IT shows all good hits as I expected from 
>>>>> the sample.
>>>>> But when I used peptide prophet, The result is all 0 probability?
>>>>> I tried merging 4 files and individually also. But in all cases the 
>>>>> probability comes to 0.
>>>>> 
>>>>> where is the problem>
>>>>> 
>>>>> Best
>>>>> 
>>>>> -- 
>>>>> You received this message because you are subscribed to the Google Groups 
>>>>> "spctools-discuss" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send an 
>>>>> email to spctools-discuss+unsubscr...@googlegroups.com 
>>>>> <mailto:spctools-discuss+unsubscr...@googlegroups.com>.
>>>>> To view this discussion on the web visit 
>>>>> https://groups.google.com/d/msgid/spctools-discuss/e74da627-d489-453c-b480-96453fbdc6a5n%40googlegroups.com
>>>>>  
>>>>> <https://groups.google.com/d/msgid/spctools-discuss/e74da627-d489-453c-b480-96453fbdc6a5n%40googlegroups.com?utm_medium=email&utm_source=footer>.
>>>> 
>>>> 
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>>>>  
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>>> 
>>> 
>>> --
>>> ---
>>> The real voyage of discovery consists not in seeking new lands but seeing 
>>> with new eyes. — Marcel Proust
>>> 
>>> Dr. Sudarshan Kumar
>>> (Fulbright-Nehru Fellow)
>>> (B.V.Sc.& A.H., M.V.Sc &

Re: [spctools-discuss] Peptide prophet showing all zero probability

['David Shteynberg' via spctools-discuss]

Can you compress the mzML file, the search database and your search
together and reshare?  I will need at least those file to try to reproduce
your process.

Cheers!

On Wed, Jul 24, 2024, 2:19 AM sudarshan kumar 
wrote:

>
>  20240417_AN_171_POS_LCMSMS_00.mzML
> <https://drive.google.com/file/d/1qNf8C08bcg0KwF56HmonihILxh3uVqyU/view?usp=drive_web>
> please find the mzml file shared through drive
>
> On Wed, Jul 24, 2024 at 12:40 AM sudarshan kumar 
> wrote:
>
>> Thank you so much  David,
>> Please find the screenshot of what I am getting.
>> I am sharing the file also for you to check please.
>> Best regards,
>> Sud
>>
>>
>> On Tue, Jul 23, 2024 at 10:16 AM David Shteynberg <
>> dshteynb...@systemsbiology.org> wrote:
>>
>>> Hello Sudarshan,
>>>
>>> Although it is not possible to tell exactly what happened here without
>>> more information, the usual suspects are:
>>>
>>> 1.  Data Quality
>>> 2.  Incorrect Database
>>> 3.  Incorrect Parameters
>>>
>>> I just ran a test of X!Tandem locally on the ISB18 dataset.  The search
>>> ran and the TPP validation generated PSMs with positive probability
>>> values.  If you are able to provide more information about your specific
>>> analysis or post your dataset online for download I would be happy to take
>>> a closer look.
>>>
>>> Cheers!
>>> -David
>>>
>>>
>>>
>>>
>>> On Jul 23, 2024, at 4:56 AM, sudarshan kumar 
>>> wrote:
>>>
>>> Hi,
>>> Can you please explain why?
>>> When I searched with tandem, IT shows all good hits as I expected from
>>> the sample.
>>> But when I used peptide prophet, The result is all 0 probability?
>>> I tried merging 4 files and individually also. But in all cases the
>>> probability comes to 0.
>>>
>>> where is the problem>
>>>
>>> Best
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discuss+unsubscr...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/e74da627-d489-453c-b480-96453fbdc6a5n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/e74da627-d489-453c-b480-96453fbdc6a5n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discuss+unsubscr...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/4E5196E2-E7D9-4B46-91CB-462A19AEFAAC%40systemsbiology.org
>>> <https://groups.google.com/d/msgid/spctools-discuss/4E5196E2-E7D9-4B46-91CB-462A19AEFAAC%40systemsbiology.org?utm_medium=email&utm_source=footer>
>>> .
>>>
>>
>>
>> --
>> ---
>> The real voyage of discovery consists not in seeking new lands but seeing
>> with new eyes. — Marcel Proust
>>
>> Dr. Sudarshan Kumar
>> (Fulbright-Nehru Fellow)
>> (B.V.Sc.& A.H., M.V.Sc., PhD.)
>> Sr. Scientist
>> Animal Biotechnology Center
>> (Proteomics and Cell Biology Lab.)
>> National Dairy Research Institute Karnal, 132001
>> Haryana, India
>> Contact No 09254912456
>> URL www.ndri.res.in
>> Orcid Id: https://orcid.org/-0002-9816-4307
>>
>>
>
> --
> ---
> The real voyage of discovery consists not in seeking new lands but seeing
> with new eyes. — Marcel Proust
>
> Dr. Sudarshan Kumar
> (Fulbright-Nehru Fellow)
> (B.V.Sc.& A.H., M.V.Sc., PhD.)
> Sr. Scientist
> Animal Biotechnology Center
> (Proteomics and Cell Biology Lab.)
> National Dairy Research Institute Karnal, 132001
> Haryana, India
> Contact No 09254912456
> URL www.ndri.res.in
> Orcid Id: https://orcid.org/-0002-9816-4307
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/CALZrgHTC2%2BQ5XagQASK5OL5zHRhaykxHYY83%2B0L%3DbHE9FkN%3DRg%40mail.gmail.com
> <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHTC2%2BQ5XagQASK5OL5zHRhaykxHYY83%2B0L%3DbHE9FkN%3DRg%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>

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Re: [spctools-discuss] Peptide prophet showing all zero probability

[David Shteynberg]

Hello Sudarshan,

Although it is not possible to tell exactly what happened here without more 
information, the usual suspects are:

1.  Data Quality
2.  Incorrect Database
3.  Incorrect Parameters

I just ran a test of X!Tandem locally on the ISB18 dataset.  The search ran and 
the TPP validation generated PSMs with positive probability values.  If you are 
able to provide more information about your specific analysis or post your 
dataset online for download I would be happy to take a closer look.

Cheers!
-David




> On Jul 23, 2024, at 4:56 AM, sudarshan kumar  wrote:
> 
> Hi, 
> Can you please explain why?
> When I searched with tandem, IT shows all good hits as I expected from the 
> sample.
> But when I used peptide prophet, The result is all 0 probability?
> I tried merging 4 files and individually also. But in all cases the 
> probability comes to 0.
> 
> where is the problem>
> 
> Best
> 
> -- 
> You received this message because you are subscribed to the Google Groups 
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to spctools-discuss+unsubscr...@googlegroups.com 
> .
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/spctools-discuss/e74da627-d489-453c-b480-96453fbdc6a5n%40googlegroups.com
>  
> .

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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

[David Shteynberg]

Zeyu,

I think I was reading your message from May, about the issue which you helped 
us identify and resolve, sorry.  Meanwhile,  I tested both MSVC default version 
of Kojak and compared to the one built for TPP using gcc and they seem 
completely equivalent in runtime.  Let me know if you observe something 
different.

Thank you,
-David

> On Jul 18, 2024, at 2:33 PM, David Shteynberg 
>  wrote:
> 
> Hello Zeyu,
> 
> Would you mind installing the latest update and report back if you still have 
> an issue here?
> 
> Thanks,
> -David
> 
> On Thu, Jul 18, 2024 at 1:35 PM Zeyu Wang  <mailto:wangzeyuu...@gmail.com>> wrote:
>> Hi David,
>> 
>> Sorry for the late reply. Later, I just left the computer running on 
>> E-cores, which took longer. Now I further tested the new kojak.exe you sent 
>> me, but it still doesn't change the default CPU usage.  
>> 
>> I believe this "feature" is due to how Windows handles task prioritization. 
>> I finally resolved it by adjusting the priority and affinity of Kojak.exe in 
>> the Windows Task Manager. 
>> 
>> Thanks for your help and advice!
>> 
>> Best,
>> Zeyu Wang
>> 
>> On Wednesday, May 29, 2024 at 10:52:42 PM UTC-4 David Shteynberg wrote:
>>> Hi Zeyu,
>>> 
>>> Thanks for testing this!  I recompiled another executable that should use 
>>> more of the CPU during the search.  Can you please test it to see if this 
>>> suits your needs?  Naturally, if you set the number of threads too high it 
>>> might degrade the overall performance of your machine during the Kojak 
>>> search.  
>>> 
>>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>> 
>>> It would interesting to compare the performance of before and after this 
>>> change.  I am testing this on i9-13900H.
>>> 
>>> Cheers,
>>> -David
>>> 
>>> On Tue, May 28, 2024 at 9:21 PM Zeyu Wang > wrote:
>>>> Hi David, 
>>>> 
>>>> I tested it with the new version. Now it works well, but CPU usage problem 
>>>> still exists. I change threads from 24, 20 to 16 and 8, but the TPP 
>>>> searching still uses E-cores. Perhaps it doesn't support P-Cores with 
>>>> Intel Hyper-Threading. I am just wondering what CPU you are using for 
>>>> Kojak.exe running. 
>>>> 
>>>> Thanks again! Anyway, it can still run, though may take a bit longer time. 
>>>> 
>>>> Best,
>>>> Zeyu 
>>>> 
>>>> On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:
>>>>> Hello Zeyu,
>>>>> 
>>>>> Sorry I don't know the answer to your question but if it helps I 
>>>>> corrected the issue you identified in the previously distributed version 
>>>>> compiled with gcc for the TPP distribution installer.
>>>>> I placed the gcc compiled version of Kojak.exe here: 
>>>>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>>>> 
>>>>> Perhaps this one exhibits a different behavior when running 
>>>>> multi-threaded.  In my tests the two version ran nearly at the same speed 
>>>>> on my computer.
>>>>> 
>>>>> Cheers,
>>>>> -David
>>>>> 
>>>>> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang > wrote:
>>>>>> Hi all,
>>>>>> 
>>>>>> I notice another small issue (maybe this is my win11 problem?): when 
>>>>>> running Kojak within TPP, I set the threads to 24 or 28. However, in the 
>>>>>> task manager, I notice the main search was always running on exact 
>>>>>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice 
>>>>>> similar problem?   
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Best,
>>>>>> Zeyu 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>>>>>> Hi David,
>>>>>>> 
>>>>>>> Thanks! After replacing the current kojak.exe, It seems that now the 
>>>>>>> koja

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

['David Shteynberg' via spctools-discuss]

Hello Zeyu,

Would you mind installing the latest update and report back if you still
have an issue here?

Thanks,
-David

On Thu, Jul 18, 2024 at 1:35 PM Zeyu Wang  wrote:

> Hi David,
>
> Sorry for the late reply. Later, I just left the computer running on
> E-cores, which took longer. Now I further tested the new kojak.exe you sent
> me, but it still doesn't change the default CPU usage.
>
> I believe this "feature" is due to how Windows handles task
> prioritization. I finally resolved it by adjusting the priority and
> affinity of Kojak.exe in the Windows Task Manager.
>
> Thanks for your help and advice!
>
> Best,
> Zeyu Wang
>
> On Wednesday, May 29, 2024 at 10:52:42 PM UTC-4 David Shteynberg wrote:
>
>> Hi Zeyu,
>>
>> Thanks for testing this!  I recompiled another executable that should use
>> more of the CPU during the search.  Can you please test it to see if this
>> suits your needs?  Naturally, if you set the number of threads too high it
>> might degrade the overall performance of your machine during the Kojak
>> search.
>>
>>
>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>
>> It would interesting to compare the performance of before and after this
>> change.  I am testing this on i9-13900H.
>>
>> Cheers,
>> -David
>>
>> On Tue, May 28, 2024 at 9:21 PM Zeyu Wang  wrote:
>>
>>> Hi David,
>>>
>>> I tested it with the new version. Now it works well, but CPU usage
>>> problem still exists. I change threads from 24, 20 to 16 and 8, but the TPP
>>> searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel
>>> Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe
>>> running.
>>>
>>> Thanks again! Anyway, it can still run, though may take a bit longer
>>> time.
>>>
>>> Best,
>>> Zeyu
>>>
>>> On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:
>>>
>>>> Hello Zeyu,
>>>>
>>>> Sorry I don't know the answer to your question but if it helps I
>>>> corrected the issue you identified in the previously distributed version
>>>> compiled with gcc for the TPP distribution installer.
>>>> I placed the gcc compiled version of Kojak.exe here:
>>>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>>>
>>>> Perhaps this one exhibits a different behavior when running
>>>> multi-threaded.  In my tests the two version ran nearly at the same speed
>>>> on my computer.
>>>>
>>>> Cheers,
>>>> -David
>>>>
>>>> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I notice another small issue (maybe this is my win11 problem?): when
>>>>> running Kojak within TPP, I set the threads to 24 or 28. However, in the
>>>>> task manager, I notice the main search was always running on exact
>>>>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice
>>>>> similar problem?
>>>>>
>>>>> [image: Snipaste_2024-05-28_22-14-14.png]
>>>>> [image: Snipaste_2024-05-28_22-15-57.png]
>>>>>
>>>>> Best,
>>>>> Zeyu
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> Thanks! After replacing the current kojak.exe, It seems that now the
>>>>>> kojak searching can continue without error message.
>>>>>>
>>>>>> Best,
>>>>>> Zeyu
>>>>>>
>>>>>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>>>>>
>>>>>>> Hello again,
>>>>>>>
>>>>>>> After a bit of digging I found that this is likely caused by a bug
>>>>>>> in the current TPP compiled and distributed version of Kojak that will 
>>>>>>> have
>>>>>>> to be corrected for the next release.  Meanwhile you should be able to
>>>>>>> download and use the official Kojak build available 

[spctools-discuss]

[David Shteynberg]

Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.1.0
"Albedo"

We are proud to offer a minor update to the Trans-Proteomic Pipeline (TPP)
software, release 7.1.0.  The software is available with installer for
MacOS, Windows; Linux and Android users can build the software from source,
from all the usual locations (please see the section below, "Getting the
TPP Software").  Current recommendations for most users is to install using
the Windows or MacOS installers, which setup and configure TPP and other
required software, such as the Apache web server, perl and python
automatically.  For advanced or enterprise users, who need to customize
TPP, or for those users who run on Linux and Android, the source code is
provided for download and the software must be configured and compiled *on
site*.  When building from source, add site specific configurations to *site.mk
 *in the top level directory after unpacking the source
tree.

== Release Notes ==
Release notes on the most important new features, changes, and known issues
are available here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.1.0_Release_Notes


== Getting the TPP Software ==
Download TPP Version 7.1.0 (Albedo) for your OS at the Sashimi SourceForge
project file release page:
https://sourceforge.net/projects/sashimi/files/latest/download

Everyone is encouraged to read and contribute to our wiki, at
  http://tools.proteomecenter.org/wiki/

For guides on building, installing and using the software, please see our
wiki:
  http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

For downloading the source code, please go to the following link:
  http://sourceforge.net/projects/sashimi/files/  and find the 7.1.0 source
code  package

or, check out the code directly from svn:
  svn export https://svn.code.sf.net/p/sashimi/code/tags/release_7-1
-0



For building from source, refer to the README and INSTALL files in src/
directory of TPP as well as the wiki.


== Acknowledgements ==
The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers who
contributed to this release from ISB.  Thanks to developers and users from
the TPP's user community who also provided feedback and code contributions.

-- 
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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

['David Shteynberg' via spctools-discuss]

Hi Zeyu,

Thanks for testing this!  I recompiled another executable that should use
more of the CPU during the search.  Can you please test it to see if this
suits your needs?  Naturally, if you set the number of threads too high it
might degrade the overall performance of your machine during the Kojak
search.

https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download

It would interesting to compare the performance of before and after this
change.  I am testing this on i9-13900H.

Cheers,
-David

On Tue, May 28, 2024 at 9:21 PM Zeyu Wang  wrote:

> Hi David,
>
> I tested it with the new version. Now it works well, but CPU usage problem
> still exists. I change threads from 24, 20 to 16 and 8, but the TPP
> searching still uses E-cores. Perhaps it doesn't support P-Cores with Intel
> Hyper-Threading. I am just wondering what CPU you are using for Kojak.exe
> running.
>
> Thanks again! Anyway, it can still run, though may take a bit longer time.
>
> Best,
> Zeyu
>
> On Tuesday, May 28, 2024 at 11:17:55 PM UTC-4 David Shteynberg wrote:
>
>> Hello Zeyu,
>>
>> Sorry I don't know the answer to your question but if it helps I
>> corrected the issue you identified in the previously distributed version
>> compiled with gcc for the TPP distribution installer.
>> I placed the gcc compiled version of Kojak.exe here:
>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download
>>
>> Perhaps this one exhibits a different behavior when running
>> multi-threaded.  In my tests the two version ran nearly at the same speed
>> on my computer.
>>
>> Cheers,
>> -David
>>
>> On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:
>>
>>> Hi all,
>>>
>>> I notice another small issue (maybe this is my win11 problem?): when
>>> running Kojak within TPP, I set the threads to 24 or 28. However, in the
>>> task manager, I notice the main search was always running on exact
>>> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice
>>> similar problem?
>>>
>>> [image: Snipaste_2024-05-28_22-14-14.png]
>>> [image: Snipaste_2024-05-28_22-15-57.png]
>>>
>>> Best,
>>> Zeyu
>>>
>>>
>>>
>>>
>>>
>>> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>>>
>>>> Hi David,
>>>>
>>>> Thanks! After replacing the current kojak.exe, It seems that now the
>>>> kojak searching can continue without error message.
>>>>
>>>> Best,
>>>> Zeyu
>>>>
>>>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>>>
>>>>> Hello again,
>>>>>
>>>>> After a bit of digging I found that this is likely caused by a bug in
>>>>> the current TPP compiled and distributed version of Kojak that will have 
>>>>> to
>>>>> be corrected for the next release.  Meanwhile you should be able to
>>>>> download and use the official Kojak build available here:
>>>>> https://kojak-ms.systemsbiology.net/download.html
>>>>>
>>>>>
>>>>> This version will require additional .net dependecies!
>>>>>
>>>>> Please replace the current kojak executable in c:/TPP/bin with the
>>>>> executable from the zip file and try running kojak again.
>>>>>
>>>>>
>>>>> Best of luck and keep us posted to your progress.
>>>>>
>>>>> -David
>>>>>
>>>>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> Thank you! Here are the two kojak parameter files I tested (the
>>>>>> original and the customized).  Link: Kojak_Troubleshooting
>>>>>> <https://gtvault-my.sharepoint.com/:f:/g/personal/zwang3136_gatech_edu/EnxqUYYUZGNDvCEG8kB-vtsB3Q2GfNvcqaAygJ_0ttBEFA?e=Ub1nub>
>>>>>>  .
>>>>>>
>>>>>> Best,
>>>>>> Zeyu
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>>>>>>
>>>>>> Hello Zeyu,
>>>>>&

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

['David Shteynberg' via spctools-discuss]

Hello Zeyu,

Sorry I don't know the answer to your question but if it helps I corrected
the issue you identified in the previously distributed version compiled
with gcc for the TPP distribution installer.
I placed the gcc compiled version of Kojak.exe here:
https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/Kojak.exe/download

Perhaps this one exhibits a different behavior when running
multi-threaded.  In my tests the two version ran nearly at the same speed
on my computer.

Cheers,
-David

On Tue, May 28, 2024 at 7:27 PM Zeyu Wang  wrote:

> Hi all,
>
> I notice another small issue (maybe this is my win11 problem?): when
> running Kojak within TPP, I set the threads to 24 or 28. However, in the
> task manager, I notice the main search was always running on exact
> CPU16-31, which seem to be E-cores of this 13900K. Did anyone notice
> similar problem?
>
> [image: Snipaste_2024-05-28_22-14-14.png]
> [image: Snipaste_2024-05-28_22-15-57.png]
>
> Best,
> Zeyu
>
>
>
>
>
> On Monday, May 27, 2024 at 11:12:09 AM UTC-4 Zeyu Wang wrote:
>
>> Hi David,
>>
>> Thanks! After replacing the current kojak.exe, It seems that now the
>> kojak searching can continue without error message.
>>
>> Best,
>> Zeyu
>>
>> On Friday, May 24, 2024 at 9:55:03 PM UTC-4 David Shteynberg wrote:
>>
>>> Hello again,
>>>
>>> After a bit of digging I found that this is likely caused by a bug in
>>> the current TPP compiled and distributed version of Kojak that will have to
>>> be corrected for the next release.  Meanwhile you should be able to
>>> download and use the official Kojak build available here:
>>> https://kojak-ms.systemsbiology.net/download.html
>>>
>>>
>>> This version will require additional .net dependecies!
>>>
>>> Please replace the current kojak executable in c:/TPP/bin with the
>>> executable from the zip file and try running kojak again.
>>>
>>>
>>> Best of luck and keep us posted to your progress.
>>>
>>> -David
>>>
>>> On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:
>>>
>>>> Hi David,
>>>>
>>>> Thank you! Here are the two kojak parameter files I tested (the
>>>> original and the customized).  Link: Kojak_Troubleshooting
>>>> <https://gtvault-my.sharepoint.com/:f:/g/personal/zwang3136_gatech_edu/EnxqUYYUZGNDvCEG8kB-vtsB3Q2GfNvcqaAygJ_0ttBEFA?e=Ub1nub>
>>>>  .
>>>>
>>>> Best,
>>>> Zeyu
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>>>>
>>>> Hello Zeyu,
>>>>
>>>> Thanks for your interest in TPP and Kojak.  Yes we maintain and use
>>>> Kojak in the latest release.  To help us troubleshoot this problem, would
>>>> you mind sharing the parameter file used in your test?
>>>>
>>>> Thank you!
>>>> -David
>>>>
>>>> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>>>>
>>>> Hi,
>>>>
>>>> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the
>>>> instruction and try to run a quick test. But at the very beginning, it
>>>> reports an error.
>>>>
>>>> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann,
>>>> Institute for Systems Biology Visit http://kojak-ms.org for full
>>>> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24
>>>> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12
>>>> preconfigured crosslinkers. Reading FASTA database:
>>>> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
>>>> ...
>>>>   Total Proteins: 20594
>>>>   Adding Kojak-generated decoys. New Total Proteins: 41188
>>>>   5658462 peptides to search (2785870 linkable).
>>>>
>>>> Fri May 24 02:52:45 2024 ERROR:
>>>> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt
>>>> for output. Please ensure path and write permissions are correct."
>>>>
>>>> Is the error due to the output file path format? Or shall I adjust the
>>>> read/write permission of the TPP?
>>>>
>>>> Best,
>>>> Zeyu
>>>>
>>>> --
>>>> You received this message because

Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

['David Shteynberg' via spctools-discuss]

Hello again,

After a bit of digging I found that this is likely caused by a bug in the
current TPP compiled and distributed version of Kojak that will have to be
corrected for the next release.  Meanwhile you should be able to download
and use the official Kojak build available here:
https://kojak-ms.systemsbiology.net/download.html


This version will require additional .net dependecies!

Please replace the current kojak executable in c:/TPP/bin with the
executable from the zip file and try running kojak again.


Best of luck and keep us posted to your progress.

-David

On Fri, May 24, 2024, 1:07 PM Zeyu Wang  wrote:

> Hi David,
>
> Thank you! Here are the two kojak parameter files I tested (the original
> and the customized).  Link: Kojak_Troubleshooting
> <https://gtvault-my.sharepoint.com/:f:/g/personal/zwang3136_gatech_edu/EnxqUYYUZGNDvCEG8kB-vtsB3Q2GfNvcqaAygJ_0ttBEFA?e=Ub1nub>
>  .
>
> Best,
> Zeyu
>
>
>
>
>
>
>
> On Friday, May 24, 2024 at 3:47:38 PM UTC-4 David Shteynberg wrote:
>
> Hello Zeyu,
>
> Thanks for your interest in TPP and Kojak.  Yes we maintain and use Kojak
> in the latest release.  To help us troubleshoot this problem, would you
> mind sharing the parameter file used in your test?
>
> Thank you!
> -David
>
> On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:
>
> Hi,
>
> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the
> instruction and try to run a quick test. But at the very beginning, it
> reports an error.
>
> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann,
> Institute for Systems Biology Visit http://kojak-ms.org for full
> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24
> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12
> preconfigured crosslinkers. Reading FASTA database:
> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
> ...
>   Total Proteins: 20594
>   Adding Kojak-generated decoys. New Total Proteins: 41188
>   5658462 peptides to search (2785870 linkable).
>
> Fri May 24 02:52:45 2024 ERROR:
> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for
> output. Please ensure path and write permissions are correct."
>
> Is the error due to the output file path format? Or shall I adjust the
> read/write permission of the TPP?
>
> Best,
> Zeyu
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discu...@googlegroups.com.
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> https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com
> <https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
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> .
>

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Re: [spctools-discuss] Issue with Kojak searching of TPP v7.0.0

['David Shteynberg' via spctools-discuss]

Hello Zeyu,

Thanks for your interest in TPP and Kojak.  Yes we maintain and use Kojak
in the latest release.  To help us troubleshoot this problem, would you
mind sharing the parameter file used in your test?

Thank you!
-David

On Fri, May 24, 2024, 12:28 AM Zeyu Wang  wrote:

> Hi,
>
> Are there anyone using Kojak in the TPP v7.0.0 ?  Today I follow the
> instruction and try to run a quick test. But at the very beginning, it
> reports an error.
>
> "Kojak version 2.1.0, October 16 2023 Copyright Michael Hoopmann,
> Institute for Systems Biology Visit http://kojak-ms.org for full
> documentation. ** Begin Kojak Analysis ** Time at start: Fri May 24
> 02:52:02 2024 Parameter file: c:/TPP/data/params/Kojak_2.conf 12
> preconfigured crosslinkers. Reading FASTA database:
> c:/TPP/data/dbase/UP05640_9606_20230222.fasta
> ...
>   Total Proteins: 20594
>   Adding Kojak-generated decoys. New Total Proteins: 41188
>   5658462 peptides to search (2785870 linkable).
>
> Fri May 24 02:52:45 2024 ERROR:
> ERROR: cannot open \c:\TPP\data\Test_Kojak\E_ZW_LPS_XL_F10.kojak.txt for
> output. Please ensure path and write permissions are correct."
>
> Is the error due to the output file path format? Or shall I adjust the
> read/write permission of the TPP?
>
> Best,
> Zeyu
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
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> https://groups.google.com/d/msgid/spctools-discuss/c1b41187-61c0-4dc2-ba42-9a997f09eb7en%40googlegroups.com
> 
> .
>

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Re: [spctools-discuss] Seeking help regarding peptide prophet and decoy mode

['David Shteynberg' via spctools-discuss]

Here is the best reference describing iProphet in detail:
https://pubmed.ncbi.nlm.nih.gov/21876204/

iProphet starts with PeptideProphet probabilities at the "PSM-level"
(always model-based) and computes the probabilities at the
"peptide-level."  It always produces one result per spectrum (whether or
not each spectrum is searched by different engines or not.)  The
probability of each peptide sequence identified by iProphet should be taken
as the maximum over all PSMs matching that peptide sequence.  I do not use
MSStatsTMT so cannot help you there.  BTW, the TPP tool for TMT and other
isobaric quantification approaches is called Libra.

To answer your Comet decoy question:  if you are using TPP's decoy
generator then you likely don't need additional decoys provided by comet,
so I would recommend to turn those OFF.

Best of luck!

-David

On Tue, May 14, 2024 at 2:08 AM Debojyoti Pal 
wrote:

> Thank you Dr David! That is really great help.
>
> I have a couple  of follow-up queries:
>
> 1) If I use iProphet on these results, does that now use Decoy based FDR
> estimates or the PeptideProphet statisitcal model only estimates.
>
> 2) If I combine multiple PeptideProphet outputs (from fractions of same
> digest) in iProphet , how does that affect individual PSMs? For example, if
> a PSM if found in multiple fractions, does it get converted to single PSM
> in the iProphet output (I just want to make the output compatible to
> MSStatsTMT - see here https://groups.google.com/g/msstats/c/aINhWMKt2Co)
> While MSStatsTMT has converters for other SW like Maxquant and PD, I kind
> of like TPP, so trying to establish a proper workflow for my fractionated
> TMT data.
>
> Thanks again,
> Debojyoti
>
> On Sunday, May 12, 2024 at 10:54:18 PM UTC+5:30 David Shteynberg wrote:
>
>> Dear Debojyoti,
>>
>> Welcome to the world of TPP!
>>
>> If you have a database of targets you can use the following tool in TPP
>> to generate random (repeat preserving deBruijn) decoys for your targets:
>>
>> [image: image.png]
>>
>> With the default options this tool will create two independent sets
>> decoys for each of your targets, prefixed by DECOY0 and DECOY1.
>>
>> After you search the data you can analyze it with PeptideProphet in many
>> different ways.  I would suggest you try with the following options to
>> start:
>>
>> [image: image.png]
>>
>> This will enable PeptideProphet to use DECOY0 hits as model-decoys and
>> DECOY1 hits as validation-decoys.
>>
>> With these setting the table on the models page will contain model-based
>> error estimations based on the model trained with DECOY0 ("known" decoys).
>>
>> As part of the run with these settings DECOY1 will be used to validate
>> the PeptideProphet model using the "unknown" decoys.  This will be
>> displayed on the models page "Models Charts" tab near the bottom, for
>> example:
>> [image: image.png]
>>
>> The chart on the right shows both the "DECOY" (DECOY1 "unknown") ROC
>> curve and the "PREDICTED" (DECOY0 "known" model-based) ROC curve.  The
>> error estimates comparing the model-based error to the unknown/validation
>> decoy-based error are on the chart on the left.  If you want evaluate a
>> model using a different decoys settings you can run the ProphetModels.pl
>> decoy validation tool on the following page:
>> [image: image.png]
>>
>> On this page set the decoy proteins to the PeptideProphet "model unknown"
>> and the excluded decoys to the PeptideProphet "model known' ones (if any)
>> as follows:
>> [image: image.png]
>>
>> Hopefully this helps you process your dataset.  Let us know if you have
>> additional questions.
>>
>> Cheers!
>> -David
>>
>>
>>
>> On Sun, May 12, 2024 at 2:38 AM Debojyoti Pal 
>> wrote:
>>
>>> Hello everyone
>>>
>>> Proteomics newbie here. I am trying to use TPP and peptide prophet but
>>> really unable to understand the options and outputs. Seeking help of the
>>> experienced members.[image: peptideprophet.PNG]
>>>
>>> What are the options that I need to activate to estimate FDR via the
>>> target-decoy mode? I am currently generation decoy through comet and
>>> actuvation "use decoy hits to pin down" option and "known protein names
>>> begin with" option and "use non parametric model option". What do the
>>> option "report decoy hits with computed probability do? And the other
>>> options too?
>>

Re: [spctools-discuss] Running MSfragger search in TPP 7.0

['David Shteynberg' via spctools-discuss]

Hi  Zeyu,

Thanks for your question and for your interest in the TPP.

Yes I use MSFragger in the TPP and I did run into this exact problem last
week.  It required me to install java 9 jdk that I downloaded and installed
from oracle.  I then had to make sure that the windows PATH pointed to the
correct version of java from the jdk.  Let me know if you cannot find it
and I would be glad to help you further.

I have found that the PeptideProphet model that seems to function best for
MSFragger searches is the EXPECTSCORE based NONPARAM (semi-supervised)
model, also with the option ONEFVAL to model all the charge states with a
single f-value mixture model.

Hope you find this useful.

Cheers!
-David

On Fri, May 10, 2024 at 3:05 PM Zeyu Wang  wrote:

> Hi,
>
> Do you use MSFragger in TPP? I downloaded MSFragger 4.0 and renamed it,
> then placed it in this path: C:/TPP/bin/msfragger/msfragger.jar. However,
> when I search my files, it seems to report an error related to the JRE
> version. But MSFragger desktop GUI runs fine:
>
> Error: A JNI error has occurred, please check your installation and try
> again.
> Exception in thread "main" java.lang.UnsupportedClassVersionError:
> edu/umich/andykong/msfragger/MSFragger has been compiled by a more recent
> version of the Java Runtime (class file version 53.0), this version of the
> Java Runtime only recognizes class file versions up to 52.0.
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClass(Unknown Source)
> at java.security.SecureClassLoader.defineClass(Unknown Source)
> at java.net.URLClassLoader.defineClass(Unknown Source)
> at java.net.URLClassLoader.access$100(Unknown Source)
> at java.net.URLClassLoader$1.run(Unknown Source)
> at java.net.URLClassLoader$1.run(Unknown Source)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source)
>
>
> Thank you!
>
> --
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> "spctools-discuss" group.
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> email to spctools-discuss+unsubscr...@googlegroups.com.
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> 
> .
>

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Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

['David Shteynberg' via spctools-discuss]

Sounds great!  Let us know should you require further help answering TPP
related questions.

On Tue, Apr 16, 2024 at 3:06 PM Robert Willows  wrote:

> Hi David,
>
> I have solved the issue. A typo in the https-tpp.config file.
> Require ip had the wrong number. I’d typed the ip address number
> incorrectly. Everything loading and running now with proper style sheet.
>
> Thanks for the help in tracking this down.
>
> Regards
> Robert
>
> On 17 Apr 2024, at 7:59 AM, 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
> 
> Hi Robert,
>
> The fact that the css is not loading is an strong indication that the
> apache configuration is not correct.
>
> I just built a 7.0.0 TPP instance on a fresh ubuntu 22.04.4 "jammy" node
> in the Azure "cloud", using instructions here:
>
>
> http://tools.proteomecenter.org/wiki/index.php?title=TPP_7.0.0:_Installing_on_Ubuntu_22.04_LTS#Configuring_the_Apache_web_server
>
> It seems to load as expected.  Sorry, but I am not sure why your specific
> instance is becoming misconfigured.  Perhaps you can launch another node in
> the cloud, try setting it up there and if you run into trouble I can log in
> and help troubleshoot?
>
> Cheers,
> -David
>
>
>
>
> On Tue, Apr 16, 2024 at 2:02 PM Robert Willows 
> wrote:
>
>> Hi David,
>>
>> The style sheet isn’t loading. Just a very basic login screen missing the
>> usual TPP style.
>> The same when running the other cgi’s from the browser/s.
>> No not serving any other sites from this server.
>>
>> Regards
>> Robert
>>
>> On 17 Apr 2024, at 12:53 AM, 'David Shteynberg' via spctools-discuss <
>> spctools-discuss@googlegroups.com> wrote:
>>
>> 
>> This seems to be a configuration issue but I am not sure where, likely in
>> the server.  It appears you are running apache 2.4.x (same as I, on my
>> phone ubuntu emulator ;) which is in configured by http-2.4-tpp.conf. This
>> file should be first configured by site.mk at make install.  You should
>> not have to modify this file, perhaps only for testing.  Is the css
>> stylesheet loading for you on the login screen?  Can you provide a
>> screenshot?  Are you serving any other sites from this server?
>>
>> Thanks!
>>
>>
>> On Mon, Apr 15, 2024, 11:50 PM Robert Willows 
>> wrote:
>>
>>> one more piece of puzzle.
>>> The httpd-tpp.conf has:
>>> ## Set the TPP's environment variables
>>> SetEnv TPP_HOME/usr/local/tpp
>>> SetEnv TPP_DATADIR /data
>>> SetEnv SEQ2MS_SOURCE_URL _SEQ2MS_SOURCE_URL_
>>> SetEnv SEQ2MS_DEFAULT_MODEL _SEQ2MS_DEFAULT_MODEL_
>>> SetEnv TPP_BASEURL /tpp
>>> SetEnv TPP_DATAURL /tpp/data
>>>
>>> When I change the TPP_BASEURL and TPP_DATAURL  to the same as in the
>>> site.mk file
>>> SetEnv TPP_BASEURL tpp
>>> SetEnv TPP_DATAURL tpp/data
>>>
>>> The login screen then goes to:
>>> http://localhost:10401/tpp/cgi-bin/tpp/cgi-bin/tpp_gui.pl
>>> Site not found.
>>> So it is adding an additional tpp/cgi-bin/ to the path after login as
>>> guest.
>>>
>>> Is this a webserver config issue or a tpp issue?
>>>
>>>
>>>
>>> On Tuesday, April 16, 2024 at 1:14:03 PM UTC+10 Robert Willows wrote:
>>>
>>>> Hi David,
>>>>
>>>> I've changed the site.mk and recompiled.
>>>> Deleted the old install in the /usr/local/tpp directory and reinstalled
>>>> withy make install.
>>>> Restarted everything but still have the same issue.
>>>>
>>>> Still goes to http://tpp/cgi-bin/tpp_gui.pl after entering guest
>>>> username and password.
>>>> I've tried some of the other cgi-bin programs in place of tpp_gui.pl
>>>> http://localhost:10401/tpp/cgi-bin/X and they all run and give
>>>> somewhat of the expected output given no files,  except for
>>>> http://localhost:10401/tpp/cgi-bin/tpp_gui_config.pl
>>>>
>>>> Internal Server Error
>>>>
>>>> The server encountered an internal error or misconfiguration and was
>>>> unable to complete your request.
>>>>
>>>> Please contact the server administrator at [no address given] to inform
>>>> them of the time this error occurred, and the actions you performed just
>>>> before this error.
>>>>
>>>> More information about t

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

['David Shteynberg' via spctools-discuss]

Hi Robert,

The fact that the css is not loading is an strong indication that the
apache configuration is not correct.

I just built a 7.0.0 TPP instance on a fresh ubuntu 22.04.4 "jammy" node in
the Azure "cloud", using instructions here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_7.0.0:_Installing_on_Ubuntu_22.04_LTS#Configuring_the_Apache_web_server

It seems to load as expected.  Sorry, but I am not sure why your specific
instance is becoming misconfigured.  Perhaps you can launch another node in
the cloud, try setting it up there and if you run into trouble I can log in
and help troubleshoot?

Cheers,
-David




On Tue, Apr 16, 2024 at 2:02 PM Robert Willows  wrote:

> Hi David,
>
> The style sheet isn’t loading. Just a very basic login screen missing the
> usual TPP style.
> The same when running the other cgi’s from the browser/s.
> No not serving any other sites from this server.
>
> Regards
> Robert
>
> On 17 Apr 2024, at 12:53 AM, 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
> 
> This seems to be a configuration issue but I am not sure where, likely in
> the server.  It appears you are running apache 2.4.x (same as I, on my
> phone ubuntu emulator ;) which is in configured by http-2.4-tpp.conf. This
> file should be first configured by site.mk at make install.  You should
> not have to modify this file, perhaps only for testing.  Is the css
> stylesheet loading for you on the login screen?  Can you provide a
> screenshot?  Are you serving any other sites from this server?
>
> Thanks!
>
>
> On Mon, Apr 15, 2024, 11:50 PM Robert Willows 
> wrote:
>
>> one more piece of puzzle.
>> The httpd-tpp.conf has:
>> ## Set the TPP's environment variables
>> SetEnv TPP_HOME/usr/local/tpp
>> SetEnv TPP_DATADIR /data
>> SetEnv SEQ2MS_SOURCE_URL _SEQ2MS_SOURCE_URL_
>> SetEnv SEQ2MS_DEFAULT_MODEL _SEQ2MS_DEFAULT_MODEL_
>> SetEnv TPP_BASEURL /tpp
>> SetEnv TPP_DATAURL /tpp/data
>>
>> When I change the TPP_BASEURL and TPP_DATAURL  to the same as in the
>> site.mk file
>> SetEnv TPP_BASEURL tpp
>> SetEnv TPP_DATAURL tpp/data
>>
>> The login screen then goes to:
>> http://localhost:10401/tpp/cgi-bin/tpp/cgi-bin/tpp_gui.pl
>> Site not found.
>> So it is adding an additional tpp/cgi-bin/ to the path after login as
>> guest.
>>
>> Is this a webserver config issue or a tpp issue?
>>
>>
>>
>> On Tuesday, April 16, 2024 at 1:14:03 PM UTC+10 Robert Willows wrote:
>>
>>> Hi David,
>>>
>>> I've changed the site.mk and recompiled.
>>> Deleted the old install in the /usr/local/tpp directory and reinstalled
>>> withy make install.
>>> Restarted everything but still have the same issue.
>>>
>>> Still goes to http://tpp/cgi-bin/tpp_gui.pl after entering guest
>>> username and password.
>>> I've tried some of the other cgi-bin programs in place of tpp_gui.pl
>>> http://localhost:10401/tpp/cgi-bin/X and they all run and give
>>> somewhat of the expected output given no files,  except for
>>> http://localhost:10401/tpp/cgi-bin/tpp_gui_config.pl
>>>
>>> Internal Server Error
>>>
>>> The server encountered an internal error or misconfiguration and was
>>> unable to complete your request.
>>>
>>> Please contact the server administrator at [no address given] to inform
>>> them of the time this error occurred, and the actions you performed just
>>> before this error.
>>>
>>> More information about this error may be available in the server error
>>> log.
>>>
>>> [Tue Apr 16 13:08:10.934308 2024] [cgid:error] [pid 841488:tid
>>> 140546230744960] (8)Exec format error: AH01241: exec of
>>> '/usr/local/tpp/cgi-bin/tpp_gui_config.pl' failed
>>>
>>> [Tue Apr 16 13:08:10.934745 2024] [cgid:error] [pid 841395:tid
>>> 140546200757824] [client ::1:38680] End of script output before headers:
>>> tpp_gui_config.pl
>>> On Tuesday, April 16, 2024 at 11:02:17 AM UTC+10 David Shteynberg wrote:
>>>
>>>> Hi Robert,
>>>>
>>>> I think I see the problem.  TPP_BASEURL and TPP_DATAURL should be
>>>> relative, no start with '/',  try changing your site.mk to :
>>>>
>>>> INSTALL_DIR = /usr/local/tpp
>>>> TPP_DATADIR = /data
>>>> TPP_BASEURL = tpp
>>>> TPP_DATAURL = tpp/data
>>>> TPP_PORT = 10401
>>>>
>>

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

['David Shteynberg' via spctools-discuss]

This seems to be a configuration issue but I am not sure where, likely in
the server.  It appears you are running apache 2.4.x (same as I, on my
phone ubuntu emulator ;) which is in configured by http-2.4-tpp.conf. This
file should be first configured by site.mk at make install.  You should not
have to modify this file, perhaps only for testing.  Is the css stylesheet
loading for you on the login screen?  Can you provide a screenshot?  Are
you serving any other sites from this server?

Thanks!


On Mon, Apr 15, 2024, 11:50 PM Robert Willows  wrote:

> one more piece of puzzle.
> The httpd-tpp.conf has:
> ## Set the TPP's environment variables
> SetEnv TPP_HOME/usr/local/tpp
> SetEnv TPP_DATADIR /data
> SetEnv SEQ2MS_SOURCE_URL _SEQ2MS_SOURCE_URL_
> SetEnv SEQ2MS_DEFAULT_MODEL _SEQ2MS_DEFAULT_MODEL_
> SetEnv TPP_BASEURL /tpp
> SetEnv TPP_DATAURL /tpp/data
>
> When I change the TPP_BASEURL and TPP_DATAURL  to the same as in the
> site.mk file
> SetEnv TPP_BASEURL tpp
> SetEnv TPP_DATAURL tpp/data
>
> The login screen then goes to:
> http://localhost:10401/tpp/cgi-bin/tpp/cgi-bin/tpp_gui.pl
> Site not found.
> So it is adding an additional tpp/cgi-bin/ to the path after login as
> guest.
>
> Is this a webserver config issue or a tpp issue?
>
>
>
> On Tuesday, April 16, 2024 at 1:14:03 PM UTC+10 Robert Willows wrote:
>
>> Hi David,
>>
>> I've changed the site.mk and recompiled.
>> Deleted the old install in the /usr/local/tpp directory and reinstalled
>> withy make install.
>> Restarted everything but still have the same issue.
>>
>> Still goes to http://tpp/cgi-bin/tpp_gui.pl after entering guest
>> username and password.
>> I've tried some of the other cgi-bin programs in place of tpp_gui.pl
>> http://localhost:10401/tpp/cgi-bin/X and they all run and give
>> somewhat of the expected output given no files,  except for
>> http://localhost:10401/tpp/cgi-bin/tpp_gui_config.pl
>>
>> Internal Server Error
>>
>> The server encountered an internal error or misconfiguration and was
>> unable to complete your request.
>>
>> Please contact the server administrator at [no address given] to inform
>> them of the time this error occurred, and the actions you performed just
>> before this error.
>>
>> More information about this error may be available in the server error
>> log.
>>
>> [Tue Apr 16 13:08:10.934308 2024] [cgid:error] [pid 841488:tid
>> 140546230744960] (8)Exec format error: AH01241: exec of
>> '/usr/local/tpp/cgi-bin/tpp_gui_config.pl' failed
>>
>> [Tue Apr 16 13:08:10.934745 2024] [cgid:error] [pid 841395:tid
>> 140546200757824] [client ::1:38680] End of script output before headers:
>> tpp_gui_config.pl
>> On Tuesday, April 16, 2024 at 11:02:17 AM UTC+10 David Shteynberg wrote:
>>
>>> Hi Robert,
>>>
>>> I think I see the problem.  TPP_BASEURL and TPP_DATAURL should be
>>> relative, no start with '/',  try changing your site.mk to :
>>>
>>> INSTALL_DIR = /usr/local/tpp
>>> TPP_DATADIR = /data
>>> TPP_BASEURL = tpp
>>> TPP_DATAURL = tpp/data
>>> TPP_PORT = 10401
>>>
>>> Then you will need to make all and make install from scratch.  The
>>> easiest way is to rename the previous build directory.
>>>
>>> Cheers!
>>> -David
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Apr 15, 2024 at 5:50 PM Robert Willows 
>>> wrote:
>>>
>>>> Hi David,
>>>>
>>>> The site.mk file is:
>>>> INSTALL_DIR = /usr/local/tpp
>>>> TPP_DATADIR = /data
>>>> TPP_BASEURL = /tpp
>>>> TPP_DATAURL = /tpp/data
>>>> TPP_PORT = 10401
>>>>
>>>> The output from http://localhost:10401/tpp/cgi-bin/check_env.pl is
>>>> HTTP_ACCEPT =
>>>> text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7
>>>> HTTP_SEC_CH_UA_PLATFORM = "Linux"
>>>> REQUEST_URI = /tpp/cgi-bin/check_env.pl
>>>> HTTP_SEC_FETCH_MODE = navigate
>>>> PATH =
>>>> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
>>>> SCRIPT_FILENAME = /usr/local/tpp/cgi-bin/check_env.pl
>>>> SERVER_SOFTWARE = Apache/2.4.52 (Ubuntu)
>>>> WEBSERVER_ROOT = /usr/local/tpp
>>>> SERVER_NAME = localhost
>>>> CONTEXT_PREFIX = //tpp/cgi-bin
>>>> REMOTE_ADDR = ::1

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

['David Shteynberg' via spctools-discuss]

Can you seen if you can access the server at:

 127.0.0.1:10401/tpp

or

 127.0.0.1:10401/tpp/cgi-bin/tpp_gui.pl

Thanks!

On Mon, Apr 15, 2024, 11:50 PM Robert Willows  wrote:

> one more piece of puzzle.
> The httpd-tpp.conf has:
> ## Set the TPP's environment variables
> SetEnv TPP_HOME/usr/local/tpp
> SetEnv TPP_DATADIR /data
> SetEnv SEQ2MS_SOURCE_URL _SEQ2MS_SOURCE_URL_
> SetEnv SEQ2MS_DEFAULT_MODEL _SEQ2MS_DEFAULT_MODEL_
> SetEnv TPP_BASEURL /tpp
> SetEnv TPP_DATAURL /tpp/data
>
> When I change the TPP_BASEURL and TPP_DATAURL  to the same as in the
> site.mk file
> SetEnv TPP_BASEURL tpp
> SetEnv TPP_DATAURL tpp/data
>
> The login screen then goes to:
> http://localhost:10401/tpp/cgi-bin/tpp/cgi-bin/tpp_gui.pl
> Site not found.
> So it is adding an additional tpp/cgi-bin/ to the path after login as
> guest.
>
> Is this a webserver config issue or a tpp issue?
>
>
>
> On Tuesday, April 16, 2024 at 1:14:03 PM UTC+10 Robert Willows wrote:
>
>> Hi David,
>>
>> I've changed the site.mk and recompiled.
>> Deleted the old install in the /usr/local/tpp directory and reinstalled
>> withy make install.
>> Restarted everything but still have the same issue.
>>
>> Still goes to http://tpp/cgi-bin/tpp_gui.pl after entering guest
>> username and password.
>> I've tried some of the other cgi-bin programs in place of tpp_gui.pl
>> http://localhost:10401/tpp/cgi-bin/X and they all run and give
>> somewhat of the expected output given no files,  except for
>> http://localhost:10401/tpp/cgi-bin/tpp_gui_config.pl
>>
>> Internal Server Error
>>
>> The server encountered an internal error or misconfiguration and was
>> unable to complete your request.
>>
>> Please contact the server administrator at [no address given] to inform
>> them of the time this error occurred, and the actions you performed just
>> before this error.
>>
>> More information about this error may be available in the server error
>> log.
>>
>> [Tue Apr 16 13:08:10.934308 2024] [cgid:error] [pid 841488:tid
>> 140546230744960] (8)Exec format error: AH01241: exec of
>> '/usr/local/tpp/cgi-bin/tpp_gui_config.pl' failed
>>
>> [Tue Apr 16 13:08:10.934745 2024] [cgid:error] [pid 841395:tid
>> 140546200757824] [client ::1:38680] End of script output before headers:
>> tpp_gui_config.pl
>> On Tuesday, April 16, 2024 at 11:02:17 AM UTC+10 David Shteynberg wrote:
>>
>>> Hi Robert,
>>>
>>> I think I see the problem.  TPP_BASEURL and TPP_DATAURL should be
>>> relative, no start with '/',  try changing your site.mk to :
>>>
>>> INSTALL_DIR = /usr/local/tpp
>>> TPP_DATADIR = /data
>>> TPP_BASEURL = tpp
>>> TPP_DATAURL = tpp/data
>>> TPP_PORT = 10401
>>>
>>> Then you will need to make all and make install from scratch.  The
>>> easiest way is to rename the previous build directory.
>>>
>>> Cheers!
>>> -David
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Apr 15, 2024 at 5:50 PM Robert Willows 
>>> wrote:
>>>
>>>> Hi David,
>>>>
>>>> The site.mk file is:
>>>> INSTALL_DIR = /usr/local/tpp
>>>> TPP_DATADIR = /data
>>>> TPP_BASEURL = /tpp
>>>> TPP_DATAURL = /tpp/data
>>>> TPP_PORT = 10401
>>>>
>>>> The output from http://localhost:10401/tpp/cgi-bin/check_env.pl is
>>>> HTTP_ACCEPT =
>>>> text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7
>>>> HTTP_SEC_CH_UA_PLATFORM = "Linux"
>>>> REQUEST_URI = /tpp/cgi-bin/check_env.pl
>>>> HTTP_SEC_FETCH_MODE = navigate
>>>> PATH =
>>>> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
>>>> SCRIPT_FILENAME = /usr/local/tpp/cgi-bin/check_env.pl
>>>> SERVER_SOFTWARE = Apache/2.4.52 (Ubuntu)
>>>> WEBSERVER_ROOT = /usr/local/tpp
>>>> SERVER_NAME = localhost
>>>> CONTEXT_PREFIX = //tpp/cgi-bin
>>>> REMOTE_ADDR = ::1
>>>> SCRIPT_URI = http://localhost:10401/tpp/cgi-bin/check_env.pl
>>>> TPP_DATADIR = /data
>>>> HTTP_CONNECTION = keep-alive
>>>> HTTP_SEC_CH_UA = "Google Chrome";v="123", "Not:A-Brand";v="8",
>>>> "Chromium";v="123"
>>>> HTTP_SEC_FETCH

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

['David Shteynberg' via spctools-discuss]

Hi Robert,

I think I see the problem.  TPP_BASEURL and TPP_DATAURL should be relative,
no start with '/',  try changing your site.mk to :

INSTALL_DIR = /usr/local/tpp
TPP_DATADIR = /data
TPP_BASEURL = tpp
TPP_DATAURL = tpp/data
TPP_PORT = 10401

Then you will need to make all and make install from scratch.  The easiest
way is to rename the previous build directory.

Cheers!
-David





On Mon, Apr 15, 2024 at 5:50 PM Robert Willows  wrote:

> Hi David,
>
> The site.mk file is:
> INSTALL_DIR = /usr/local/tpp
> TPP_DATADIR = /data
> TPP_BASEURL = /tpp
> TPP_DATAURL = /tpp/data
> TPP_PORT = 10401
>
> The output from http://localhost:10401/tpp/cgi-bin/check_env.pl is
> HTTP_ACCEPT =
> text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7
> HTTP_SEC_CH_UA_PLATFORM = "Linux"
> REQUEST_URI = /tpp/cgi-bin/check_env.pl
> HTTP_SEC_FETCH_MODE = navigate
> PATH =
> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
> SCRIPT_FILENAME = /usr/local/tpp/cgi-bin/check_env.pl
> SERVER_SOFTWARE = Apache/2.4.52 (Ubuntu)
> WEBSERVER_ROOT = /usr/local/tpp
> SERVER_NAME = localhost
> CONTEXT_PREFIX = //tpp/cgi-bin
> REMOTE_ADDR = ::1
> SCRIPT_URI = http://localhost:10401/tpp/cgi-bin/check_env.pl
> TPP_DATADIR = /data
> HTTP_CONNECTION = keep-alive
> HTTP_SEC_CH_UA = "Google Chrome";v="123", "Not:A-Brand";v="8",
> "Chromium";v="123"
> HTTP_SEC_FETCH_USER = ?1
> REQUEST_METHOD = GET
> SCRIPT_NAME = /tpp/cgi-bin/check_env.pl
> SEQ2MS_SOURCE_URL = _SEQ2MS_SOURCE_URL_
> SCRIPT_URL = /tpp/cgi-bin/check_env.pl
> HTTP_ACCEPT_ENCODING = gzip, deflate, br, zstd
> SERVER_SIGNATURE =Apache/2.4.52 (Ubuntu) Server at localhost Port 10401
> HTTP_USER_AGENT = Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36
> (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36
> REMOTE_PORT = 49404
> TPP_BASEURL = //tpp
> TPP_DATAURL = //tpp/data
> USERPROFILE = /usr/local/tpp
> GATEWAY_INTERFACE = CGI/1.1
> HTTP_HOST = localhost:10401
> CONTEXT_DOCUMENT_ROOT = /usr/local/tpp/cgi-bin
> HTTP_ACCEPT_LANGUAGE = en-GB,en-US;q=0.9,en;q=0.8
> PERL5LIB = /usr/local/tpp/lib/perl
> DOCUMENT_ROOT = /var/www/html
> REQUEST_SCHEME = http
> SEQ2MS_DEFAULT_MODEL = _SEQ2MS_DEFAULT_MODEL_
> QUERY_STRING =
> SERVER_ADMIN = [no address given]
> HTTP_SEC_FETCH_SITE = none
> WEBSERVER_TMP = /tmp
> SERVER_PROTOCOL = HTTP/1.1
> HTTP_UPGRADE_INSECURE_REQUESTS = 1
> HTTP_SEC_FETCH_DEST = document
> SERVER_PORT = 10401
> SERVER_ADDR = ::1
> SSRCALC = /usr/local/tpp/conf
> HTTP_SEC_CH_UA_MOBILE = ?0
> TPP_HOME = /usr/local/tpp
>
>
>
>
> On Tuesday, April 16, 2024 at 12:01:17 AM UTC+10 David Shteynberg wrote:
>
> Hi Robert,
>
> Thanks for trying to install and use TPP on Ubuntu.  It seems the
> webserver is somewhat misconfigured for tpp on your system.  Can you share
> the site.mk file that you are using for this build as this file allows to
> control the PATHs and URLS used by TPP?
>
> Thanks!
> -David
>
>
> On Mon, Apr 15, 2024, 1:08 AM Robert Willows  wrote:
>
>
> I just finished building and installing TPP 7.0 under Ubuntu. All appears
> well until I go to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
>
> The login appears:
> ISB/SPC Trans Proteomic Pipeline ::
> .
>  TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)
>
> But after entering guest as username and password the pages goes to:
> http://tpp/cgi-bin/tpp_gui.pl
> and
> This site can’t be reached
>
> Check if there is a typo in tpp.
> DNS_PROBE_FINISHED_NXDOMAIN
>
> Apache error logs are empty and access log is:
> 127.0.1.1:80 ::1 - - [15/Apr/2024:17:47:01 +1000] "GET /tpp/cgi-bin/
> tpp_gui.pl HTTP/1.1" 200 1076 "-" "Mozilla/5.0 (X11; Linux x86_64)
> AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36"
> 127.0.1.1:80 ::1 - - [15/Apr/2024:17:47:53 +1000] "-" 408 0 "-" "-"
>
> Any help or incites as I feel I've exhausted possibilities.
>
>
>
>
>
>
>
>
>
>
>  TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)
>
> --
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> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discu...@googlegroups.com.
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> <https://groups.google.com/d/msgid/spctools-discuss/efaa2e37-f

Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

[David Shteynberg]

To further troubleshoot you can try running the environment checker on the
tpp server using the following url on your machine:

http://localhost:10401/tpp/cgi-bin/check_env.pl

This should give you an idea how the tpp environment is configured from the
web server’s perspective and perhaps help identify any missing environment
variables, specifically HTTP_HOST should be set to "localhost" based on the
installation you described.

To print the tpp_hostname (HTTP_HOST) that is configured in your tpp
installation you can run the command "tpp_hostname" on the commandline.

Good luck!
-David



On Apr 15, 2024, at 7:01 AM, David Shteynberg <
david.shteynb...@isbscience.org> wrote:

Hi Robert,

Thanks for trying to install and use TPP on Ubuntu.  It seems the webserver
is somewhat misconfigured for tpp on your system.  Can you share the site.mk
file that you are using for this build as this file allows to control the
PATHs and URLS used by TPP?

Thanks!
-David


On Mon, Apr 15, 2024, 1:08 AM Robert Willows  wrote:

>
> I just finished building and installing TPP 7.0 under Ubuntu. All appears
> well until I go to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
>
> The login appears:
> ISB/SPC Trans Proteomic Pipeline ::
> .
>  TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)
>
> But after entering guest as username and password the pages goes to:
> http://tpp/cgi-bin/tpp_gui.pl
> and
> This site can’t be reached
>
> Check if there is a typo in tpp.
> DNS_PROBE_FINISHED_NXDOMAIN
>
> Apache error logs are empty and access log is:
> 127.0.1.1:80 <http://127.0.1.1/> ::1 - - [15/Apr/2024:17:47:01 +1000]
> "GET /tpp/cgi-bin/tpp_gui.pl HTTP/1.1" 200 1076 "-" "Mozilla/5.0 (X11;
> Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0
> Safari/537.36"
> 127.0.1.1:80 <http://127.0.1.1/> ::1 - - [15/Apr/2024:17:47:53 +1000] "-"
> 408 0 "-" "-"
>
> Any help or incites as I feel I've exhausted possibilities.
>
>
>
>
>
>
>
>
>
>
>  TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/efaa2e37-fa8a-482a-aeda-4bb044a6b5ean%40googlegroups.com
> <https://groups.google.com/d/msgid/spctools-discuss/efaa2e37-fa8a-482a-aeda-4bb044a6b5ean%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>

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Re: [spctools-discuss] TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

['David Shteynberg' via spctools-discuss]

Hi Robert,

Thanks for trying to install and use TPP on Ubuntu.  It seems the webserver
is somewhat misconfigured for tpp on your system.  Can you share the site.mk
file that you are using for this build as this file allows to control the
PATHs and URLS used by TPP?

Thanks!
-David


On Mon, Apr 15, 2024, 1:08 AM Robert Willows  wrote:

>
> I just finished building and installing TPP 7.0 under Ubuntu. All appears
> well until I go to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
>
> The login appears:
> ISB/SPC Trans Proteomic Pipeline ::
> .
>  TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)
>
> But after entering guest as username and password the pages goes to:
> http://tpp/cgi-bin/tpp_gui.pl
> and
> This site can’t be reached
>
> Check if there is a typo in tpp.
> DNS_PROBE_FINISHED_NXDOMAIN
>
> Apache error logs are empty and access log is:
> 127.0.1.1:80 ::1 - - [15/Apr/2024:17:47:01 +1000] "GET /tpp/cgi-bin/
> tpp_gui.pl HTTP/1.1" 200 1076 "-" "Mozilla/5.0 (X11; Linux x86_64)
> AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36"
> 127.0.1.1:80 ::1 - - [15/Apr/2024:17:47:53 +1000] "-" 408 0 "-" "-"
>
> Any help or incites as I feel I've exhausted possibilities.
>
>
>
>
>
>
>
>
>
>
>  TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/efaa2e37-fa8a-482a-aeda-4bb044a6b5ean%40googlegroups.com
> 
> .
>

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Re: [spctools-discuss] Lib2HTML truncates peptide sequences after modification

[David Shteynberg]

Excellent! Thank you for letting me know.

> On Apr 11, 2024, at 9:12 AM, 'Juergen Bartel' via spctools-discuss 
>  wrote:
> 
> Hi David,
> 
> Thank you for modifying the code so quickly! I have just tested Lib2HTML with 
> the new prerelease and it works perfectly fine now.
> 
> Cheers!
> Juergen
> 
> David Shteynberg schrieb am Donnerstag, 11. April 2024 um 02:28:19 UTC+2:
>> Hello Juergen,
>> 
>> Thanks for providing the test data.  I was able to modify the code to allow 
>> Lib2HTML to also read the user modifications and display the from the HTML 
>> page.  The prerelease installer that has this feature is available here:  
>> 
>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/TPP_Setup_7.0.x.exe/download
>> 
>> Let me know if you have any other questions.
>> 
>> Cheers!
>> -David
>> 
>> T
>> 
>> On Fri, Apr 5, 2024 at 1:45 AM 'Juergen Bartel' via spctools-discuss 
>> > wrote:
>>> Dear David,
>>> 
>>> to generate my library I have done a couple of steps:
>>> 1) modified the file utils.py from seq2ms to contain my modifications:
>>> # C H N O S P
>>> # mods = {"ox" : [0,0,0,1,0,0], ## changed this line to enable sulfatase 
>>> modification prediction se=serine; al=formylglycine-aldehyd; 
>>> do=formylglycine-diol; ds=diol-sulfate; ss=serine-sulfate
>>> mods = {"ox" : [0,0,0,1,0,0], "se" : [0,0,1,0,-1,0], "al" : 
>>> [0,-2,1,0,-1,0], "do" : [0,0,2,0,-1,0], "ds" : [0,-1,5,0,0,0], "ss" : 
>>> [0,0,4,0,0,0],
>>> "ph" : [0,1,0,3,0,1], 
>>> "cam" : [2,3,1,1,0,0] , "ac": [2,2,0,1,0,0], "me": [1,2,0,0,0,0], 
>>> "hy": [0,0,0,1,0,0], "gly": [4,6,2,2,0,0],
>>> "bi" : [10,14,2,2,1,0], "cr": [4,4,0,1,0,0], "di": [2,4,0,0,0,0], 
>>> "ma": [3,2,0,3,0,0], "ni": [0,-1,1,2,0,0],
>>> "bu" : [4,6,0,1,0,0], "fo": [1,0,0,1,0,0], "glu": [5,6,0,3,0,0], 
>>> "hyb": [4,6,0,2,0,0], "pr": [3,4,0,1,0,0],
>>> "su" : [4,4,0,3,0,0], "tr": [3,6,0,0,0,0], "ci": [0,-1,-1,1,0,0]}
>>> 
>>> 2) I run the prediction by executing 'predict.py' with the a modified 
>>> input.tsv and (I think) the pretrained_model. The input file looked like 
>>> the following but contained more peptides:
>>> SequenceCharge  MassModified sequence   ModificationProtein
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2   3332.613578 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_   Unmodified  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3   3332.613576 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_   Unmodified  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4   3332.613576 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_   Unmodified  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2   3316.636422 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_   Serine (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3   3316.636422 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_   Serine (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4   3316.63642  
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_   Serine (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2   3314.620772 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_   FGAldehyd (C)   
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3   3314.62077  
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_   FGAldehyd (C)   
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4   3314.620772 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_   FGAldehyd (C)   
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2   3332.631336 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_   FGDiol (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3   3332.631336 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_   FGDiol (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4   3332.631336 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_   FGDiol (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2   3411.580326 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_   DiolSulfat (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3   3411.580326 
>>> _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_   DiolSulfat (C)  
>>> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4

Re: [spctools-discuss] Re: Lib2HTML truncates peptide sequences after modification

['David Shteynberg' via spctools-discuss]

Hello Juergen,

Thanks for providing the test data.  I was able to modify the code to allow
Lib2HTML to also read the user modifications and display the from the HTML
page.  The prerelease installer that has this feature is available here:

https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v7.0%20%28Arafel%29%20rev%20X/TPP_Setup_7.0.x.exe/download

Let me know if you have any other questions.

Cheers!
-David

T

On Fri, Apr 5, 2024 at 1:45 AM 'Juergen Bartel' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> Dear David,
>
> to generate my library I have done a couple of steps:
> 1) modified the file utils.py from seq2ms to contain my modifications:
>
>
>
>
>
>
>
> *# C H N O S P# mods = {"ox" : [0,0,0,1,0,0], ## changed this line to
> enable sulfatase modification prediction se=serine;
> al=formylglycine-aldehyd; do=formylglycine-diol; ds=diol-sulfate;
> ss=serine-sulfatemods = {"ox" : [0,0,0,1,0,0], "se" : [0,0,1,0,-1,0], "al"
> : [0,-2,1,0,-1,0], "do" : [0,0,2,0,-1,0], "ds" : [0,-1,5,0,0,0], "ss" :
> [0,0,4,0,0,0],"ph" : [0,1,0,3,0,1], "cam" : [2,3,1,1,0,0] ,
> "ac": [2,2,0,1,0,0], "me": [1,2,0,0,0,0], "hy": [0,0,0,1,0,0], "gly":
> [4,6,2,2,0,0],"bi" : [10,14,2,2,1,0], "cr": [4,4,0,1,0,0], "di":
> [2,4,0,0,0,0], "ma": [3,2,0,3,0,0], "ni": [0,-1,1,2,0,0],"bu" :
> [4,6,0,1,0,0], "fo": [1,0,0,1,0,0], "glu": [5,6,0,3,0,0], "hyb":
> [4,6,0,2,0,0], "pr": [3,4,0,1,0,0],"su" : [4,4,0,3,0,0], "tr":
> [3,6,0,0,0,0], "ci": [0,-1,-1,1,0,0]}*
>
> 2) I run the prediction by executing 'predict.py' with the a modified
> input.tsv and (I think) the pretrained_model. The input file looked like
> the following but contained more peptides:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Sequence Charge Mass Modified sequence Modification
> ProteinDILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3332.613578
> _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_ Unmodified
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3332.613576
> _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_ Unmodified
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3332.613576
> _DILTPELDNLAQNGSIFTSAYVAHPFCGPSR_ Unmodified
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3316.636422
> _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_ Serine (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3316.636422
> _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_ Serine (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3316.63642
> _DILTPELDNLAQNGSIFTSAYVAHPFC(se)GPSR_ Serine (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3314.620772
> _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_ FGAldehyd (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3314.62077
> _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_ FGAldehyd (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3314.620772
> _DILTPELDNLAQNGSIFTSAYVAHPFC(al)GPSR_ FGAldehyd (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3332.631336
> _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_ FGDiol (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3332.631336
> _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_ FGDiol (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3332.631336
> _DILTPELDNLAQNGSIFTSAYVAHPFC(do)GPSR_ FGDiol (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3411.580326
> _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_ DiolSulfat (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3411.580326
> _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_ DiolSulfat (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3411.580324
> _DILTPELDNLAQNGSIFTSAYVAHPFC(ds)GPSR_ DiolSulfat (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 2 3396.593236
> _DILTPELDNLAQNGSIFTSAYVAHPFC(ss)GPSR_ SerinSulfat (C)
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 3 3396.593235
> _DILTPELDNLAQNGSIFTSAYVAHPFC(ss)GPSR_ Unmodified
> DILTPELDNLAQNGSIFTSAYVAHPFCGPSR 4 3396.593236
> _DILTPELDNLAQNGSIFTSAYVAHPFC(ss)GPSR_ Unmodified *
>
> 3) I imported the generated .msp file into spectraST format using the
> command line and the following options:
> *C:\TPP\bin\spectrast.exe -cNPredicted_Sec2MS.splib -MSec2MS.usermods
> Predicted.msp*
>
> 4) I tried to visualise this library by Lib2HTML from the within Petunia
>
> For the files I will send you a link via the ISB contact form to our
> university's nextcloud where I have uploaded them.
>
> Best regards,
> Juergen
>
>
> Juergen Bartel schrieb am Montag, 22. Januar 2024 um 18:22:49 UTC+1:
>
>> Dear all,
>>
>> I have recently generated an in-silico spectral library for several
>> peptides which may contains different modifications on the same cystein
>> (cystein converted to a serin, formylglycin-aldehyde, ...). For this
>> prediction I used Seq2MS (
>> https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00180) and obtained a
>> library in msp format.
>> In this file the header indicates modifications for examle in the
>> following way:
>>
>> Name: DILTPELDNLAQNGSIFTSAYVAHPFCGPSR/2_1(26,C,FGAldehyd)
>> Comment: Charge=2 Parent=1657.310386 Mods=1(26,C,FGAldehyd) Protein=nan
>>
>> If I correctly specify the modifications in a .usermods file(*) and
>> import it to spectraST, the resulting sptxt files contain header such as:
>>
>> Name: DILTPELDNLAQNGSIFTSAYVAHPFC[85]GPSR/2
>> LibID: 6
>> MW: 3316.6353
>> PrecursorMZ: 1658.3

Re: [spctools-discuss] Issue with MSConvert of TPP v7.0.0.

['David Shteynberg' via spctools-discuss]

Natchiket,

Alternatively to setting the environment PATH, you should be able to run
msconvert on the commandline by using the full path to the executable
instead, (and remember to include the quotes!)
This is the full path on my system, and likely also on yours:
"c:\Program Files\ProteoWizard\ProteoWizard 3.0.23233.c72ce16\msconvert"

[image: image.png]

Cheers!
-David

On Fri, Apr 5, 2024 at 11:07 AM David Shteynberg <
david.shteynb...@isbscience.org> wrote:

> Hello Nachiket,
>
> Thanks for your interest in the TPP!  The location where proteowizard is
> installed on your system is not in your windows system PATH environment
> variable.  Please add the directory where you found msconvert to your PATH
> environment variable and try running it again.  Let us know how it goes.
>
> Cheers!
> -David
>
> On Fri, Apr 5, 2024, 11:01 AM Nachiket W  wrote:
>
>> Hello everybody,
>>
>> I've been trying to run MSConvert from the Windows Command Prompt but it
>> keeps giving an error saying 'msconvert' is not recognized as the name of
>> cmdlet. I tried using variations like- 'MSconvert', 'msConvert',
>> 'MSConvert' to no avail.
>>
>> I also tried to look for the application in the /TPP/bin folder, the only
>> file I can locate of MSConvert is a shortcut stored in
>> C:\ProgramData\Microsoft\Windows\Start Menu\Programs\ProteoWizard
>> 3.0.23233 64-bit
>> I am running the TPP version 7.0.0. on Windows 11.
>>
>> PFA an image of the command prompt error.
>>
>> Kindly assist me in solving this issue.
>>
>> Regards,
>> Nachiket.[image: MSConvert-Error.png]
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to spctools-discuss+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/b254648b-27d4-495c-8af7-5ebea133b303n%40googlegroups.com
>> <https://groups.google.com/d/msgid/spctools-discuss/b254648b-27d4-495c-8af7-5ebea133b303n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>

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Re: [spctools-discuss] Issue with MSConvert of TPP v7.0.0.

['David Shteynberg' via spctools-discuss]

Hello Nachiket,

Thanks for your interest in the TPP!  The location where proteowizard is
installed on your system is not in your windows system PATH environment
variable.  Please add the directory where you found msconvert to your PATH
environment variable and try running it again.  Let us know how it goes.

Cheers!
-David

On Fri, Apr 5, 2024, 11:01 AM Nachiket W  wrote:

> Hello everybody,
>
> I've been trying to run MSConvert from the Windows Command Prompt but it
> keeps giving an error saying 'msconvert' is not recognized as the name of
> cmdlet. I tried using variations like- 'MSconvert', 'msConvert',
> 'MSConvert' to no avail.
>
> I also tried to look for the application in the /TPP/bin folder, the only
> file I can locate of MSConvert is a shortcut stored in
> C:\ProgramData\Microsoft\Windows\Start Menu\Programs\ProteoWizard
> 3.0.23233 64-bit
> I am running the TPP version 7.0.0. on Windows 11.
>
> PFA an image of the command prompt error.
>
> Kindly assist me in solving this issue.
>
> Regards,
> Nachiket.[image: MSConvert-Error.png]
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/b254648b-27d4-495c-8af7-5ebea133b303n%40googlegroups.com
> 
> .
>

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Re: [spctools-discuss] TPP 7.0.0 Release is now available

[David Shteynberg]

Now that I have also read your original message... sorry, I somehow missed that 
message originally.  I have used Lib2HTML to successfully convert a spectral 
library to an HTML page, although I do remember having some issues with 
unrecognized modifications when I first tried.  Lib2HTML is a completely 
separate tool from Seq2MS and uses a different code base.  The version of the 
Seq2MS software in the TPP is somewhat different from the original version and 
includes more PTMs encoded.  So this is still a bit of a work in progress with 
the PTMs and I would be happy to help you further if you can share your input 
files so I can reproduce the problem.   Seq2MS in the TPP distribution 
currently supports the subset of proforma mods pasted below.

Cheers!

Oxidation Phospho TMT Silac Carbamyl Carbamidomethyl Acetyl Methyl 
Hydroxylation GlyGly Biotinylation Crotonyl Dimethyl Malonyl Nitro 
Butyryl Formyl Gluratylation hydroxyisobutyryl Propionyl Succinyl 
Trimethyl Deamidated Gln->pyro-Glu Glu->pyro-Glu



> On Apr 4, 2024, at 6:59 AM, David Shteynberg 
>  wrote:
> 
> Hello Juergen,
> 
> Thank you for your question and use of TPP! Seq2MS's support in TPP is brand 
> new. Truncation at the PTM usually indicates that the modification was not 
> recognized or encoded in the model you applied.  Can you tell me the model 
> you applied and the modification you were searching?
> 
> Thanks!
> David
> 
> On Thu, Apr 4, 2024, 2:19 AM 'Juergen Bartel' via spctools-discuss 
>  <mailto:spctools-discuss@googlegroups.com>> wrote:
>> Dear TPP Team,
>> 
>> Thanks for generating the new TPP version. Just a question concerning the 
>> release notes: These state that Seq2MS was added. Does that also mean that 
>> the issue I mentioned some time ago with Lib2HTML ([This topic] 
>> <https://groups.google.com/g/spctools-discuss/c/3Sa9QZXAWWU/m/qHZ4LEEOAQAJ>; 
>> when peptides with multiple different modification variants are present on 
>> the same residue, it did truncate the peptides after the modified residue) 
>> was solved?
>> 
>> Best regards,
>> Juergen
>> 
>> 
>> 
>> David Shteynberg schrieb am Samstag, 30. März 2024 um 02:47:30 UTC+1:
>>> Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0
>>> Arafel
>>> 
>>> We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) 
>>> software, release 7.0.0.  The software is available for MacOS, Windows, 
>>> Linux, as well as Android from all the usual locations (please see the 
>>> section below,
>>> Getting the TPP Software
>>> ).  We recommend for most users to use the Windows or MacOS installer, 
>>> which installs and configures TPP and other required software, such as the 
>>> Apache web server, perl, and python.  For advanced users, who need to 
>>> customize TPP, or for those users who run on Linux or Android, the source 
>>> code should be downloaded and the software configured and compiled.  If 
>>> building from source, please add your site specific configuration to 
>>> site.mk <http://site.mk/> in the top level directory after unpacking the 
>>> source-code.
>>> 
>>> == Highlights ==
>>> + MacOS two-click install!
>>> + Python Support and addition of Seq2MS for Generative AI of Peptide 
>>> Fragment Spectra
>>> + Native Support of Kojak for Cross-linked Peptide Search
>>> + Native Support of Magnum for Open-mass Peptide Search
>>> + StPeter Quantification
>>> by run
>>> or
>>> by experiment
>>> + Easy to access PeptideProphet VMC model for rare-PTMs
>>> 
>>> 
>>> == Release Notes ==
>>> Release notes on the most important new features, changes, and known issues 
>>> are available at:
>>>  
>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.0.0_Release_Notes
>>> 
>>> 
>>> == Getting the TPP Software ==
>>> Download the TPP version 7.0.0 native windows installer from the Sashimi 
>>> SourceForge project file release page:
>>> https://sourceforge.net/projects/sashimi/files/latest/download
>>> 
>>> Everyone is encouraged to read and contribute to our wiki, at
>>>   http://tools.proteomecenter.org/wiki/
>>> 
>>> For guides to installing and using our software, please see our wiki:
>>>   http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
>>> 
>>> For downloading the source code, please go to the following link:
>>>   http://sourceforge.net/projects/sashimi/files/  and find the 7

Re: [spctools-discuss] Re: TPP 7.0.0 Release is now available

['David Shteynberg' via spctools-discuss]

Hello Juergen,

Thank you for your question and use of TPP! Seq2MS's support in TPP is
brand new. Truncation at the PTM usually indicates that the modification
was not recognized or encoded in the model you applied.  Can you tell me
the model you applied and the modification you were searching?

Thanks!
David

On Thu, Apr 4, 2024, 2:19 AM 'Juergen Bartel' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> Dear TPP Team,
>
> Thanks for generating the new TPP version. Just a question concerning the
> release notes: These state that Seq2MS was added. Does that also mean that
> the issue I mentioned some time ago with Lib2HTML ([This topic]
> <https://groups.google.com/g/spctools-discuss/c/3Sa9QZXAWWU/m/qHZ4LEEOAQAJ>;
> when peptides with multiple different modification variants are present on
> the same residue, it did truncate the peptides after the modified residue)
> was solved?
>
> Best regards,
> Juergen
>
>
>
> David Shteynberg schrieb am Samstag, 30. März 2024 um 02:47:30 UTC+1:
>
>> Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0
>> "Arafel"
>>
>> We are proud to offer a major update to the Trans-Proteomic Pipeline
>> (TPP) software, release 7.0.0.  The software is available for MacOS,
>> Windows, Linux, as well as Android from all the usual locations (please see
>> the section below, "Getting the TPP Software").  We recommend for most
>> users to use the Windows or MacOS installer, which installs and configures
>> TPP and other required software, such as the Apache web server, perl, and
>> python.  For advanced users, who need to customize TPP, or for those users
>> who run on Linux or Android, the source code should be downloaded and the
>> software configured and compiled.  If building from source, please add your
>> site specific configuration to site.mk in the top level directory after
>> unpacking the source-code.
>>
>> == Highlights ==
>> + MacOS two-click install!
>> + Python Support and addition of Seq2MS for Generative AI of Peptide
>> Fragment Spectra
>> + Native Support of Kojak for Cross-linked Peptide Search
>> + Native Support of Magnum for Open-mass Peptide Search
>> + StPeter Quantification "by run" or "by experiment"
>> + Easy to access PeptideProphet VMC model for rare-PTMs
>>
>>
>> == Release Notes ==
>> Release notes on the most important new features, changes, and known
>> issues are available at:
>>
>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.0.0_Release_Notes
>>
>>
>> == Getting the TPP Software ==
>> Download the TPP version 7.0.0 native windows installer from the Sashimi
>> SourceForge project file release page:
>> https://sourceforge.net/projects/sashimi/files/latest/download
>>
>> Everyone is encouraged to read and contribute to our wiki, at
>>   http://tools.proteomecenter.org/wiki/
>>
>> For guides to installing and using our software, please see our wiki:
>>   http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
>>
>> For downloading the source code, please go to the following link:
>>   http://sourceforge.net/projects/sashimi/files/  and find the 7.0.0
>> source code  package
>> or, check out the code directly from svn:
>>   svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_7-0-0
>>
>> For building from source, please refer to the README and INSTALL files in
>> top level source directory of the TPP code tree as well as the wiki.
>>
>>
>> == Acknowledgements ==
>> The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers
>> who contributed to this release from ISB.  Thanks to developers and users
>> from the TPP's user community who also provided feedback and code
>> contributions.
>>
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[spctools-discuss] TPP 7.0.0 Release is now available

['David Shteynberg' via spctools-discuss]

Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0
"Arafel"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 7.0.0.  The software is available for MacOS, Windows,
Linux, as well as Android from all the usual locations (please see the
section below, "Getting the TPP Software").  We recommend for most users to
use the Windows or MacOS installer, which installs and configures TPP and
other required software, such as the Apache web server, perl, and python.
For advanced users, who need to customize TPP, or for those users who run
on Linux or Android, the source code should be downloaded and the software
configured and compiled.  If building from source, please add your site
specific configuration to site.mk in the top level directory after
unpacking the source-code.

== Highlights ==
+ MacOS two-click install!
+ Python Support and addition of Seq2MS for Generative AI of Peptide
Fragment Spectra
+ Native Support of Kojak for Cross-linked Peptide Search
+ Native Support of Magnum for Open-mass Peptide Search
+ StPeter Quantification "by run" or "by experiment"
+ Easy to access PeptideProphet VMC model for rare-PTMs


== Release Notes ==
Release notes on the most important new features, changes, and known issues
are available at:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.0.0_Release_Notes


== Getting the TPP Software ==
Download the TPP version 7.0.0 native windows installer from the Sashimi
SourceForge project file release page:
https://sourceforge.net/projects/sashimi/files/latest/download

Everyone is encouraged to read and contribute to our wiki, at
  http://tools.proteomecenter.org/wiki/

For guides to installing and using our software, please see our wiki:
  http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

For downloading the source code, please go to the following link:
  http://sourceforge.net/projects/sashimi/files/  and find the 7.0.0 source
code  package
or, check out the code directly from svn:
  svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_7-0-0

For building from source, please refer to the README and INSTALL files in
top level source directory of the TPP code tree as well as the wiki.


== Acknowledgements ==
The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers who
contributed to this release from ISB.  Thanks to developers and users from
the TPP's user community who also provided feedback and code contributions.

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[spctools-discuss] Bug Discovery in decoyFastaGenerator.pl

['David Shteynberg' via spctools-discuss]

Dear TPP Users,

We have recently discovered and patched a bug in the TPP tool
*decoyFastaGenerator.p*l.  The bug manifests by excluding the last sequence
from the input protein database from both randomization and output, instead
outputting the penultimate protein sequence twice.

The next official release of the TPP will be patched.  Meanwhile, you can
replace the impacted program currently installed (in
*C:/TPP/bin/decoyFastaGenerator.pl* or where you installed your TPP tools)
with the code from our source tree:
*https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/perl/bin/decoyFastaGenerator.pl
*

For more information about the bug and the code change see:

*https://sourceforge.net/p/sashimi/code/9095/
*

Thank you for your continued reliance on the TPP and our efforts to provide
the proteomics community with powerful tools for your analysis and
validation needs. If you have any questions or problem please let us on
this list.

Cheers!
-David

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Re: [spctools-discuss] Trouble converting Waters.RAW with TPP msconvert

[David Shteynberg]

Hello Alex,

This is pointing to a bug in either the Waters library for access to the raw 
data or in msconvert. Perhaps you can contact Waters and msconvert developers 
to see if they have patched the problem.  My suspicion as to the nature of the 
problem is use of signed (as opposed to unsigned) variables internally for the 
representation of intensities.  Once the intensities get large enough they roll 
over to the negative representations of the values in C++.  Let us know when 
you find a solution to this issue!

Thanks,
-David

> On Jan 10, 2024, at 4:24 AM, Alex Gao  wrote:
> 
> Hi David, 
> 
> I do not know why. The data was acquired on MassLynx by a Waters Xevo QTOF 
> set to fast DDA, with scan times of MS1 and MS2 set to both 1s with 10 MS2 
> scans. The lockspray mass is also included. The settings, besides the scan 
> times, were not changed from the last time I ran the data, which worked the 
> last time. On MassLynx, the intensities look normal as well, with a dome of 
> increasing intensities over the gradient, typical of bottom up proteomics. Is 
> there a way to solve this? 
> 
> On Wednesday, January 10, 2024 at 1:56:19 AM UTC+1 David Shteynberg wrote:
>> Hello Alex,
>> 
>> I was able to download your file, convert the data to mzML using msconvert 
>> and read a few spectra using the command line tool readMzXml (works on mzML 
>> too).  Unfortunately, I am finding many intensities these files that are 
>> encoded with negative values, which is likely causing problems for the 
>> downstream tools like comet.  Do you know why negative intensities are in 
>> these files?  It is possible this is a bug with the raw encoding.  Are you 
>> able to visualize these files using Waters software to check the intensities 
>> and compare to those output by msconvert?
>> 
>> Thanks,
>> -David
>> 
>> 
>>> On Jan 5, 2024, at 4:17 AM, Alex Gao > wrote:
>>> 
>> 
>>> Hi David,
>>> 
>>> Thank you for your prompt feedback! The file can be found at the link 
>>> below. 
>>> 
>>> https://drive.google.com/file/d/1QulcwZ3UP7pcMtECNwubd4DysqaDq4UN/view?usp=sharing
>>> 
>>> Looking forward to your inputs!
>>> 
>>> Best,
>>> Alex
>>> 
>>> On Friday, January 5, 2024 at 1:09:03 AM UTC+1 David Shteynberg wrote:
>>>> Hello Alex,
>>>> 
>>>> Thanks for trying the TPP pipeline to solve your proteomics computational 
>>>> needs.  Sorry, you are having trouble converting and analyzing Waters raw 
>>>> data.  Have you tried using the latest version of msconvert to do the 
>>>> conversion to mzML?  If you are able to upload your file to an online 
>>>> drive and give me access to it, I can pull it down and try to convert it 
>>>> myself.  Let me know what works for you.
>>>> 
>>>> Cheers!
>>>> -David
>>>> 
>>>> 
>>>>> On Jan 3, 2024, at 4:32 AM, Alex Gao > wrote:
>>>>> 
>>>> 
>>>>> Hi guys, 
>>>>> 
>>>>> So I've used TPP before to convert bottom up proteomic Thermo raw files 
>>>>> in msconvert, comet search with custom params file, and xinteract to 
>>>>> perform protein prophet with no issues. Earlier this year, I performed 
>>>>> the same with Waters. Raw file, although in the beginning there was an 
>>>>> issue with size, shrinking the size of my raw file from 25 to 5-6GB did 
>>>>> the trick. 
>>>>> 
>>>>> However, recently, I reinstalled TPP (v6.3.3), and was trying to perform 
>>>>> the same task to convert 5-6GB of Waters.raw but failed. msconvert didn't 
>>>>> fail, but comet search was finished in less than 1min, which is not quite 
>>>>> right. And out of the 200,000 spectra in the original file, only 1000 ish 
>>>>> was used for comet search. this obviously leads to an error code of 256 
>>>>> at the xinteract level. 
>>>>> 
>>>>> I tried several different troubleshoots, not changing the default params 
>>>>> file except for location of fasta file, uninstalling and reinstalling, 
>>>>> changing a computer, renaming the FUNC0003 files from my Water.raw 
>>>>> directory for the search, etc. etc., but none work. 
>>>>> 
>>>>> Any help would be much appreciated. Thank you!
>>>>> 
>>>>> Best,
>>>>> Alex
>>>>> 
>>>> 
>>>>&

Re: [spctools-discuss] Trouble converting Waters.RAW with TPP msconvert

[David Shteynberg]

Hello Alex,

I was able to download your file, convert the data to mzML using msconvert and 
read a few spectra using the command line tool readMzXml (works on mzML too).  
Unfortunately, I am finding many intensities these files that are encoded with 
negative values, which is likely causing problems for the downstream tools like 
comet.  Do you know why negative intensities are in these files?  It is 
possible this is a bug with the raw encoding.  Are you able to visualize these 
files using Waters software to check the intensities and compare to those 
output by msconvert?

Thanks,
-David

> On Jan 5, 2024, at 4:17 AM, Alex Gao  wrote:
> 
> Hi David,
> 
> Thank you for your prompt feedback! The file can be found at the link below. 
> 
> https://drive.google.com/file/d/1QulcwZ3UP7pcMtECNwubd4DysqaDq4UN/view?usp=sharing
> 
> Looking forward to your inputs!
> 
> Best,
> Alex
> 
> On Friday, January 5, 2024 at 1:09:03 AM UTC+1 David Shteynberg wrote:
>> Hello Alex,
>> 
>> Thanks for trying the TPP pipeline to solve your proteomics computational 
>> needs.  Sorry, you are having trouble converting and analyzing Waters raw 
>> data.  Have you tried using the latest version of msconvert to do the 
>> conversion to mzML?  If you are able to upload your file to an online drive 
>> and give me access to it, I can pull it down and try to convert it myself.  
>> Let me know what works for you.
>> 
>> Cheers!
>> -David
>> 
>> 
>>> On Jan 3, 2024, at 4:32 AM, Alex Gao > wrote:
>>> 
>> 
>>> Hi guys, 
>>> 
>>> So I've used TPP before to convert bottom up proteomic Thermo raw files in 
>>> msconvert, comet search with custom params file, and xinteract to perform 
>>> protein prophet with no issues. Earlier this year, I performed the same 
>>> with Waters. Raw file, although in the beginning there was an issue with 
>>> size, shrinking the size of my raw file from 25 to 5-6GB did the trick. 
>>> 
>>> However, recently, I reinstalled TPP (v6.3.3), and was trying to perform 
>>> the same task to convert 5-6GB of Waters.raw but failed. msconvert didn't 
>>> fail, but comet search was finished in less than 1min, which is not quite 
>>> right. And out of the 200,000 spectra in the original file, only 1000 ish 
>>> was used for comet search. this obviously leads to an error code of 256 at 
>>> the xinteract level. 
>>> 
>>> I tried several different troubleshoots, not changing the default params 
>>> file except for location of fasta file, uninstalling and reinstalling, 
>>> changing a computer, renaming the FUNC0003 files from my Water.raw 
>>> directory for the search, etc. etc., but none work. 
>>> 
>>> Any help would be much appreciated. Thank you!
>>> 
>>> Best,
>>> Alex
>>> 
>> 
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>> 
> 
> 
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Re: [spctools-discuss] Trouble converting Waters.RAW with TPP msconvert

[David Shteynberg]

Hello Alex,

Thanks for trying the TPP pipeline to solve your proteomics computational 
needs.  Sorry, you are having trouble converting and analyzing Waters raw data. 
 Have you tried using the latest version of msconvert to do the conversion to 
mzML?  If you are able to upload your file to an online drive and give me 
access to it, I can pull it down and try to convert it myself.  Let me know 
what works for you.

Cheers!
-David

> On Jan 3, 2024, at 4:32 AM, Alex Gao  wrote:
> 
> Hi guys, 
> 
> So I've used TPP before to convert bottom up proteomic Thermo raw files in 
> msconvert, comet search with custom params file, and xinteract to perform 
> protein prophet with no issues. Earlier this year, I performed the same with 
> Waters. Raw file, although in the beginning there was an issue with size, 
> shrinking the size of my raw file from 25 to 5-6GB did the trick. 
> 
> However, recently, I reinstalled TPP (v6.3.3), and was trying to perform the 
> same task to convert 5-6GB of Waters.raw but failed. msconvert didn't fail, 
> but comet search was finished in less than 1min, which is not quite right. 
> And out of the 200,000 spectra in the original file, only 1000 ish was used 
> for comet search. this obviously leads to an error code of 256 at the 
> xinteract level. 
> 
> I tried several different troubleshoots, not changing the default params file 
> except for location of fasta file, uninstalling and reinstalling, changing a 
> computer, renaming the FUNC0003 files from my Water.raw directory for the 
> search, etc. etc., but none work. 
> 
> Any help would be much appreciated. Thank you!
> 
> Best,
> Alex
> 
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Re: [spctools-discuss] Hi I cannot access the gui anymore is there something I'm missing

[David Shteynberg]

Thank you for that.  Normally you would know the version installed based on the 
filename of the installer you ran.  Where you installed the TPP there 
should be a bin directory (default: C:/TPP/bin).   Find this location in 
Windows Explorer and find the file called tpptray.bat.

Double-click on this script to execute (you will be prompted for administrator 
credentials, which you have to provide). At this point, if all works you will 
have a TPP Service Monitor in your Windows tray.  In there you can do a few 
things like check the version number and control the web server used by the 
TPP. Click “Start TPP web server” and then your original localhost URL should 
work.  You can go there by clicking “Open TPP web interface” in the Windows TPP 
Tray.
 

I hope that works!

Cheers,
-David 


> On Dec 5, 2023, at 12:47 PM, Aarthie Senathirajah  
> wrote:
> 
> Its a windows, 
> How do I check which version I have? 
> 
> On Tue, 5 Dec 2023 at 14:57, 'David Shteynberg' via spctools-discuss 
>  <mailto:spctools-discuss@googlegroups.com>> wrote:
>> Is this windows, linux, mac?  Which version of the TPP software did you 
>> download and install?
>> 
>> On Tue, Dec 5, 2023 at 11:35 AM Aarthie Senathirajah 
>> mailto:animallover@gmail.com>> wrote:
>>> Hi David, 
>>> Thank you for your reply!
>>> This is my OS 64-bit operating system, x64-based processor
>>> But how do I check what version I have of TPP?
>>> 
>>> Thank you, 
>>> Aarthie
>>> 
>>> On Mon, 4 Dec 2023 at 17:54, David Shteynberg 
>>> mailto:dshteynb...@systemsbiology.org>> 
>>> wrote:
>>>> Hello,
>>>> 
>>>> If you could provide some additional information such as: your operating 
>>>> system, which version you installed and relevant configuration during 
>>>> installation, that would be helpful in troubleshooting your issue.  
>>>> 
>>>> Thanks!
>>>> -David
>>>> 
>>>>> On Dec 4, 2023, at 2:21 PM, Aarthie Senathirajah 
>>>>> mailto:animallover@gmail.com>> wrote:
>>>>> 
>>>>> Hi I keep clicking on the TPP link and I get the same problem. 
>>>>> Is there some file that I am missing? 
>>>>> http://localhost:10401/tpp
>>>>> 
>>>>> Any help would be appreciated
>>>>> 
>>>>> 
>>>>> On Friday, December 1, 2023 at 3:49:51 PM UTC-5 Aarthie Senathirajah 
>>>>> wrote:
>>>>>> This site can’t be reachedlocalhost refused to connect.
>>>>>> Try:
>>>>>> 
>>>>>> Checking the connection
>>>>>> Checking the proxy and the firewall <>
>>>>>> ERR_CONNECTION_REFUSED
>>>>> 
>>>>> 
>>>>> -- 
>>>>> You received this message because you are subscribed to the Google Groups 
>>>>> "spctools-discuss" group.
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>>>>> email to spctools-discuss+unsubscr...@googlegroups.com 
>>>>> <mailto:spctools-discuss+unsubscr...@googlegroups.com>.
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>>>>> https://groups.google.com/d/msgid/spctools-discuss/77b8bb93-5333-4357-a6d1-46963d5842f4n%40googlegroups.com
>>>>>  
>>>>> <https://groups.google.com/d/msgid/spctools-discuss/77b8bb93-5333-4357-a6d1-46963d5842f4n%40googlegroups.com?utm_medium=email&utm_source=footer>.
>>>> 
>>>> 
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>>>>  
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Re: [spctools-discuss] Hi I cannot access the gui anymore is there something I'm missing

['David Shteynberg' via spctools-discuss]

Is this windows, linux, mac?  Which version of the TPP software did you
download and install?

On Tue, Dec 5, 2023 at 11:35 AM Aarthie Senathirajah <
animallover@gmail.com> wrote:

> Hi David,
> Thank you for your reply!
> This is my OS 64-bit operating system, x64-based processor
> But how do I check what version I have of TPP?
>
> Thank you,
> Aarthie
>
> On Mon, 4 Dec 2023 at 17:54, David Shteynberg <
> dshteynb...@systemsbiology.org> wrote:
>
>> Hello,
>>
>> If you could provide some additional information such as: your operating
>> system, which version you installed and relevant configuration during
>> installation, that would be helpful in troubleshooting your issue.
>>
>> Thanks!
>> -David
>>
>> On Dec 4, 2023, at 2:21 PM, Aarthie Senathirajah <
>> animallover@gmail.com> wrote:
>>
>> Hi I keep clicking on the TPP link and I get the same problem.
>> Is there some file that I am missing?
>> http://localhost:10401/tpp
>>
>> Any help would be appreciated
>>
>>
>> On Friday, December 1, 2023 at 3:49:51 PM UTC-5 Aarthie Senathirajah
>> wrote:
>>
>>> This site can’t be reached
>>>
>>> *localhost* refused to connect.
>>>
>>> Try:
>>>
>>>- Checking the connection
>>>- Checking the proxy and the firewall
>>>
>>> ERR_CONNECTION_REFUSED
>>>
>>
>> --
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>> "spctools-discuss" group.
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>> email to spctools-discuss+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/77b8bb93-5333-4357-a6d1-46963d5842f4n%40googlegroups.com
>> <https://groups.google.com/d/msgid/spctools-discuss/77b8bb93-5333-4357-a6d1-46963d5842f4n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>>
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>> <https://groups.google.com/d/msgid/spctools-discuss/91A6BF78-5DA3-40E9-B20A-E8CC49718884%40systemsbiology.org?utm_medium=email&utm_source=footer>
>> .
>>
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Re: [spctools-discuss] running ASAPratio for SILAC data

['David Shteynberg' via spctools-discuss]

Of course, I am glad to help.  The old and the new versions should run
faster on the centroided data.  There is no way to tell *a priori* with
ASAPRatio how long it will take, but since it ran to completion on my
machine and it generates one dot per ten PSMs it has processed; based on
the dots you can see how much of the ASAPRatio processing has completed.
Here are the dots from my run on your data:

[image: image.png]

On Mon, Dec 4, 2023 at 2:57 PM sudarshan kumar 
wrote:

> Thank you so much David for doing this for me. In fact I was running
> asapratio again on the centroid mzml file. But I see that though express
> completed easily but the asapratio is still running. Is there any way in
> tpp to see how much time will it take to complete.
>
> But I will try with the version you have shared the link with me. Should I
> use centroid mzml for this ?.
>
> Regards, Sudarshan
>
> On Mon, Dec 4, 2023, 2:29 PM 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello Sudarshan, again!
>>
>> I was able to update the ASAPRatioPeptideParser.exe tool for your testing
>> purposes to see if it runs a bit faster after some optimization I was able
>> to implement.  Please download the following version:
>> https://drive.google.com/file/d/1Pe1pBFZ9BOxrrYNY6O8rkrybKaGtDhZZ/view?usp=sharing
>>
>> And replace the copy you have in C:/TPP/bin/
>>
>> When I ran it on my not very powerful desktop computer it completed on
>> your data in about 42,000 seconds using the new code (less than 12 hours)
>>
>> [image: image.png]
>>
>>
>> Notice that the interface still says that "This command is still
>> running..." even though the log says "job completed"
>>
>> This is because for very long jobs the webserver times-out before the job
>> completes.  To solve this the user must click the link just above that is
>> next to the text: "If you commands have actually completed but the server
>> timed out, click here"
>>
>> I hope this helps you process your data given your current computational
>> resources in less than 1 day.
>>
>> Cheers!
>> -David
>>
>> On Mon, Dec 4, 2023 at 11:05 AM sudarshan kumar 
>> wrote:
>>
>>> one more query-
>>> I used same samples - for label free and SILAC express?
>>> Ideally I should get a similar conclusion from both the experiments.
>>> But the differentially expressed proteins are different in the two
>>> analyses.
>>>
>>> NOte: I have used only one run file of control and one run file of
>>> treatment for LFQ
>>> While for SILAC I have used 6 run files of same samples (technical
>>> replicates).
>>>
>>> Please let me know where I am wrong? In my point of view increasing the
>>> number of run files will improve PSM and hence quantification using
>>> express. What should i believe my SILAC express results or the same
>>> sample LFQ (st. peters results)?
>>>
>>>
>>> On Mon, Dec 4, 2023 at 10:58 AM sudarshan kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
>>>> Hi David,
>>>> I am using this tutorial for Expressan dASAPratio . can yuo please
>>>> comment on if I am using the right one.?
>>>> Regards,
>>>> Sud
>>>>
>>>> On Thu, Nov 30, 2023 at 10:53 AM sudarshan kumar <
>>>> kumarsuders...@gmail.com> wrote:
>>>>
>>>>> can i select all the three options?
>>>>> Will it impact Express analysis?
>>>>> Centroid all scans (MS1 and MS2) -- meaningful only if data was
>>>>> acquired in profile mode
>>>>> Compress peak lists for smaller output file
>>>>> Write the output as a gzipped file (other TPP tools can read gzipped
>>>>> files directly)
>>>>>
>>>>> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
>>>>> dshteynb...@systemsbiology.org> wrote:
>>>>>
>>>>>> Dear Sud,
>>>>>>
>>>>>> I was able to process your dataset!  Although, I am still working on
>>>>>> getting a faster version of ASAPRatio compiled for your testing purposes.
>>>>>> Meanwhile you can help the process by filtering your files so that zero
>>>>>> intensity peaks in the MS1 data are removed and the MS1 data is
>>>>>> centroided.  You can accomplish both of these things using the msconvert
>>>>>> tool.  This will help reduce the time

Re: [spctools-discuss] Hi I cannot access the gui anymore is there something I'm missing

[David Shteynberg]

Hello,

If you could provide some additional information such as: your operating 
system, which version you installed and relevant configuration during 
installation, that would be helpful in troubleshooting your issue.  

Thanks!
-David

> On Dec 4, 2023, at 2:21 PM, Aarthie Senathirajah  
> wrote:
> 
> Hi I keep clicking on the TPP link and I get the same problem. 
> Is there some file that I am missing? 
> http://localhost:10401/tpp
> 
> Any help would be appreciated
> 
> 
> On Friday, December 1, 2023 at 3:49:51 PM UTC-5 Aarthie Senathirajah wrote:
>> This site can’t be reachedlocalhost refused to connect.
>> Try:
>> 
>> Checking the connection
>> Checking the proxy and the firewall <>
>> ERR_CONNECTION_REFUSED
> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups 
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to spctools-discuss+unsubscr...@googlegroups.com 
> .
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/spctools-discuss/77b8bb93-5333-4357-a6d1-46963d5842f4n%40googlegroups.com
>  
> .

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Re: [spctools-discuss] running ASAPratio for SILAC data

['David Shteynberg' via spctools-discuss]

Hello Sudarshan, again!

I was able to update the ASAPRatioPeptideParser.exe tool for your testing
purposes to see if it runs a bit faster after some optimization I was able
to implement.  Please download the following version:
https://drive.google.com/file/d/1Pe1pBFZ9BOxrrYNY6O8rkrybKaGtDhZZ/view?usp=sharing

And replace the copy you have in C:/TPP/bin/

When I ran it on my not very powerful desktop computer it completed on your
data in about 42,000 seconds using the new code (less than 12 hours)

[image: image.png]


Notice that the interface still says that "This command is still
running..." even though the log says "job completed"

This is because for very long jobs the webserver times-out before the job
completes.  To solve this the user must click the link just above that is
next to the text: "If you commands have actually completed but the server
timed out, click here"

I hope this helps you process your data given your current computational
resources in less than 1 day.

Cheers!
-David

On Mon, Dec 4, 2023 at 11:05 AM sudarshan kumar 
wrote:

> one more query-
> I used same samples - for label free and SILAC express?
> Ideally I should get a similar conclusion from both the experiments.
> But the differentially expressed proteins are different in the two
> analyses.
>
> NOte: I have used only one run file of control and one run file of
> treatment for LFQ
> While for SILAC I have used 6 run files of same samples (technical
> replicates).
>
> Please let me know where I am wrong? In my point of view increasing the
> number of run files will improve PSM and hence quantification using
> express. What should i believe my SILAC express results or the same
> sample LFQ (st. peters results)?
>
>
> On Mon, Dec 4, 2023 at 10:58 AM sudarshan kumar 
> wrote:
>
>> Hi David,
>> I am using this tutorial for Expressan dASAPratio . can yuo please
>> comment on if I am using the right one.?
>> Regards,
>> Sud
>>
>> On Thu, Nov 30, 2023 at 10:53 AM sudarshan kumar <
>> kumarsuders...@gmail.com> wrote:
>>
>>> can i select all the three options?
>>> Will it impact Express analysis?
>>> Centroid all scans (MS1 and MS2) -- meaningful only if data was acquired
>>> in profile mode
>>> Compress peak lists for smaller output file
>>> Write the output as a gzipped file (other TPP tools can read gzipped
>>> files directly)
>>>
>>> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
>>> dshteynb...@systemsbiology.org> wrote:
>>>
>>>> Dear Sud,
>>>>
>>>> I was able to process your dataset!  Although, I am still working on
>>>> getting a faster version of ASAPRatio compiled for your testing purposes.
>>>> Meanwhile you can help the process by filtering your files so that zero
>>>> intensity peaks in the MS1 data are removed and the MS1 data is
>>>> centroided.  You can accomplish both of these things using the msconvert
>>>> tool.  This will help reduce the time requirement to process this dataset.
>>>> I should have more to say about this particular case in the next few days.
>>>>
>>>> Cheers!
>>>> -David
>>>>
>>>> On Nov 29, 2023, at 10:17 AM, sudarshan kumar 
>>>> wrote:
>>>>
>>>> Hi David,
>>>> could you get time to see into my analysis? I need your advice.
>>>> Best regards,
>>>> Sud
>>>>
>>>> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss
>>>>  wrote:
>>>>
>>>>> Hello Sudarshan,
>>>>>
>>>>> Please zip this directory on your system:
>>>>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>>>>>
>>>>> Then upload the zip file to your favorite cloud server and share the
>>>>> link with me.
>>>>>
>>>>> Thanks!
>>>>> -David
>>>>>
>>>>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
>>>>> kumarsuders...@gmail.com> wrote:
>>>>>
>>>>>> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c:
>>>>>> && C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
>>>>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
>>>>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
>>>>>> 110623_Sud_LH_TEST_02.pep.xml*
>>>>>>
>>>>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan

Re: [spctools-discuss] running ASAPratio for SILAC data

['David Shteynberg' via spctools-discuss]

Hopefully, I am understanding your queries correctly, here goes.
Centroiding the data will reduce the number of peaks in the spectra and
reduce the running time of the analysis.  Compressing the files to make
them smaller will require that the tools reading the files uncompress the
data (usually internally) prior to using it which will increase the running
time.  As far as affecting the results, compressing the files should not
change the data while centroiding will. As far as how much this will affect
the final ratios probably depends on the quality of centroiding algorithm
and the quality of the data.  Run some tests yourself and get a feel on
some data you know well;  testing should help you refine your approach.
Hope that helps!

-David

On Mon, Dec 4, 2023, 10:59 AM sudarshan kumar 
wrote:

> Hi David,
> I am using this tutorial for Expressan dASAPratio . can yuo please
> comment on if I am using the right one.?
> Regards,
> Sud
>
> On Thu, Nov 30, 2023 at 10:53 AM sudarshan kumar 
> wrote:
>
>> can i select all the three options?
>> Will it impact Express analysis?
>> Centroid all scans (MS1 and MS2) -- meaningful only if data was acquired
>> in profile mode
>> Compress peak lists for smaller output file
>> Write the output as a gzipped file (other TPP tools can read gzipped
>> files directly)
>>
>> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
>> dshteynb...@systemsbiology.org> wrote:
>>
>>> Dear Sud,
>>>
>>> I was able to process your dataset!  Although, I am still working on
>>> getting a faster version of ASAPRatio compiled for your testing purposes.
>>> Meanwhile you can help the process by filtering your files so that zero
>>> intensity peaks in the MS1 data are removed and the MS1 data is
>>> centroided.  You can accomplish both of these things using the msconvert
>>> tool.  This will help reduce the time requirement to process this dataset.
>>> I should have more to say about this particular case in the next few days.
>>>
>>> Cheers!
>>> -David
>>>
>>> On Nov 29, 2023, at 10:17 AM, sudarshan kumar 
>>> wrote:
>>>
>>> Hi David,
>>> could you get time to see into my analysis? I need your advice.
>>> Best regards,
>>> Sud
>>>
>>> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss <
>>> spctools-discuss@googlegroups.com> wrote:
>>>
>>>> Hello Sudarshan,
>>>>
>>>> Please zip this directory on your system:
>>>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>>>>
>>>> Then upload the zip file to your favorite cloud server and share the
>>>> link with me.
>>>>
>>>> Thanks!
>>>> -David
>>>>
>>>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
>>>> kumarsuders...@gmail.com> wrote:
>>>>
>>>>> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c:
>>>>> && C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
>>>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
>>>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
>>>>> 110623_Sud_LH_TEST_02.pep.xml*
>>>>>
>>>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
>>>>> kumarsuders...@gmail.com> wrote:
>>>>>
>>>>>> Thank you so much David,
>>>>>> But can you tell me how can i compress? Do you mean this link?
>>>>>> (6) ISB/SPC Trans Proteomic Pipeline :: jobs
>>>>>> <http://localhost:10401/tpp/cgi-bin/tpp_gui.pl?Action=display&page=jobs&show_job=HGYB4F2HW2_20231120-150857>
>>>>>>
>>>>>> On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via
>>>>>> spctools-discuss  wrote:
>>>>>>
>>>>>>> Dear Sudarshan,
>>>>>>>
>>>>>>> It is hard to say why this particular execution resulted in apparent
>>>>>>> failure, but if you are willing to compress the *whole directory *of
>>>>>>> this analysis and send me a download link, I would be happy to download
>>>>>>> this dataset and check why it failed.
>>>>>>>
>>>>>>> Cheers!
>>>>>>> -David
>>>>>>>
>>>>>>> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar <
>>>>>>> kumarsuders...@gmail.c

Re: [spctools-discuss] running ASAPratio for SILAC data

[David Shteynberg]

Dear Sud,

I was able to process your dataset!  Although, I am still working on getting a 
faster version of ASAPRatio compiled for your testing purposes.  Meanwhile you 
can help the process by filtering your files so that zero intensity peaks in 
the MS1 data are removed and the MS1 data is centroided.  You can accomplish 
both of these things using the msconvert tool.  This will help reduce the time 
requirement to process this dataset.  I should have more to say about this 
particular case in the next few days.

Cheers!
-David

> On Nov 29, 2023, at 10:17 AM, sudarshan kumar  
> wrote:
> 
> Hi David,
> could you get time to see into my analysis? I need your advice.
> Best regards,
> Sud
> 
> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss 
>  <mailto:spctools-discuss@googlegroups.com>> wrote:
>> Hello Sudarshan,
>> 
>> Please zip this directory on your system: 
>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>> 
>> Then upload the zip file to your favorite cloud server and share the link 
>> with me.
>> 
>> Thanks!
>> -David
>> 
>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar > <mailto:kumarsuders...@gmail.com>> wrote:
>>> EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c: && 
>>> C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6 
>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199 
>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml 
>>> 110623_Sud_LH_TEST_02.pep.xml
>>> 
>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar >> <mailto:kumarsuders...@gmail.com>> wrote:
>>>> Thank you so much David,
>>>> But can you tell me how can i compress? Do you mean this link?
>>>> (6) ISB/SPC Trans Proteomic Pipeline :: jobs 
>>>> <http://localhost:10401/tpp/cgi-bin/tpp_gui.pl?Action=display&page=jobs&show_job=HGYB4F2HW2_20231120-150857>
>>>> 
>>>> On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via spctools-discuss 
>>>> >>> <mailto:spctools-discuss@googlegroups.com>> wrote:
>>>>> Dear Sudarshan,
>>>>> 
>>>>> It is hard to say why this particular execution resulted in apparent 
>>>>> failure, but if you are willing to compress the whole directory of this 
>>>>> analysis and send me a download link, I would be happy to download this 
>>>>> dataset and check why it failed.
>>>>> 
>>>>> Cheers!
>>>>> -David
>>>>> 
>>>>> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar 
>>>>> mailto:kumarsuders...@gmail.com>> wrote:
>>>>>> Can anyone please help me know, why when I am running express and 
>>>>>> ASAPratio it always takes more than two days time and though express is 
>>>>>> completed but after running for around 80% in asapratio it stucks and 
>>>>>> shows only the running status but nothing moves ahead.  >>>>> 2023-11-22 120242.png>
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> -- 
>>>>>> You received this message because you are subscribed to the Google 
>>>>>> Groups "spctools-discuss" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>>>> an email to spctools-discuss+unsubscr...@googlegroups.com 
>>>>>> <mailto:spctools-discuss+unsubscr...@googlegroups.com>.
>>>>>> To view this discussion on the web visit 
>>>>>> https://groups.google.com/d/msgid/spctools-discuss/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com
>>>>>>  
>>>>>> <https://groups.google.com/d/msgid/spctools-discuss/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com?utm_medium=email&utm_source=footer>.
>>>>> 
>>>>> 
>>>>> -- 
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>>>>> email to spctools-discuss+unsubscr...@googlegroups.com 
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Re: [spctools-discuss] sud silac asapratio

['David Shteynberg' via spctools-discuss]

You will also need to shared the mzML file containing the data.

Thanks!


On Wed, Nov 22, 2023 at 4:07 PM sudarshan kumar 
wrote:

>  interact_silaccomtwofiles.pep.zip
> 
>
>
> --
> ---
> The real voyage of discovery consists not in seeking new lands but seeing
> with new eyes. — Marcel Proust
>
> Dr. Sudarshan Kumar
> (Fulbright-Nehru Fellow)
> (B.V.Sc.& A.H., M.V.Sc., PhD.)
> Sr. Scientist
> Animal Biotechnology Center
> (Proteomics and Cell Biology Lab.)
> National Dairy Research Institute Karnal, 132001
> Haryana, India
> Contact No 09254912456
> URL www.ndri.res.in
> Orcid Id: https://orcid.org/-0002-9816-4307
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/CALZrgHTc_iCrRsyveZmtaG%2B%2B9W5mMS7kQF%2Bj5Hd-7PPp0ghfAA%40mail.gmail.com
> 
> .
>

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Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

[David Shteynberg]

Thanks Longping, I got your files.

> On Nov 17, 2023, at 5:21 PM, Longping Fu  wrote:
> 
> Dear David,
> 
> I appreciate your swift response. I've compressed the pepXML and mzML files 
> and uploaded them to Google Drive. You can access them through the following 
> link: 
> https://drive.google.com/file/d/1P463uxdvw67ZI7axiZO1OZOIlEZZg5qh/view?usp=sharing
> 
> Kindly confirm if you can successfully open the files.
> 
> Additionally, I'll be following your suggestion to include all variable 
> modifications and check for any remaining warning messages.
> 
> Thank you for your assistance.
> 
> Sincerely,
> Longping
> 
> 在2023年11月17日星期五 UTC-5 16:20:11 写道：
> Dear Longping,
> 
> Maybe you can compress your analysis pepXML and mzML files and post them 
> somewhere so I can replicate the issue locally?
> 
> Meanwhile, you can try the specifying all variable mods used in the search, 
> when you run PTMProphet by changing the modification string as follows:
>  M:15.9949,n:42.1016,STC:299.123,C:57.02146
> 
> 
> Cheers!
> 
> -David
> 
> 
> 
> 
> On Fri, Nov 17, 2023 at 1:02 PM Longping Fu > wrote:
> I am currently working with PTMProphet in TPP version 6.3.3 for PTM 
> localization. While PTMProphet successfully completes the task, I am 
> encountering a significant number of warning messages in the console.
> 
> To provide some context, my workflow involves utilizing MSFragger as the 
> search engine to convert raw files to mzML files and then searching against a 
> database. For the modification parameters, I have set M 15.9949, N-term 
> 42.1016, STC 299.123, and C 57.02146 as variable modifications, with no fixed 
> modifications specified.
> 
> Upon obtaining the pepXML file from MSFragger, I employed Percolator for PSM 
> validation using the following settings: --only-psms --no-terminate 
> --post-processing-tdc. The resulting pepxml file was then processed with 
> PTMProphet using the command: STC:299.123 MINPROB=0.5 MODPREC=0 FRAGPPMTOL=15 
> NOSTACK MAXTHREADS=1. 
> 
> However, during the PTMProphet processing, I encountered warning messages 
> similar to the following:
> 
> [WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> S[386]CNGGSHPR
>   Neutral Mass (from pepXML) = 1254.52
>   BAD (SpectraST::Peptide) = S[386]CNGGSHPR
>   Neutral Computed Mass for Evaluation = 1212.51
>   PPM difference = 33487.5
> [INFO:] please check your specified modification masses for precision or 
> adjust MODPREC= parameter ...
> [WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> SC[402]NGGSHPR
>   Neutral Mass (from pepXML) = 1254.52
>   BAD (SpectraST::Peptide) = SC[402]NGGSHPR
>   Neutral Computed Mass for Evaluation = 1212.51
>   PPM difference = 33487.5
> [INFO:] please check your specified modification masses for precision or 
> adjust MODPREC= parameter ...
> [WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: 
> SCNGGS[386]HPR
>   Neutral Mass (from pepXML) = 1254.52
>   BAD (SpectraST::Peptide) = SCNGGS[386]HPR
>   Neutral Computed Mass for Evaluation = 1212.51
>   PPM difference = 33487.5
> [INFO:] please check your specified modification masses for precision or 
> adjust MODPREC= parameter ...
> 
> This pattern repeats for various peptides, indicating that PTMProphet is 
> struggling to localize modifications on S, T, or C. The tool suggests 
> adjusting parameters, specifically the MODPREC= parameter.
> 
> Has anyone encountered a similar issue with PTMProphet and successfully 
> addressed it? I would greatly appreciate any insights, advice, or suggestions 
> regarding this matter.
> 
> -- 
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> "spctools-discuss" group.
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> email to spctools-discu...@googlegroups.com <>.
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> https://groups.google.com/d/msgid/spctools-discuss/ae1adab3-5501-4f29-b9d2-44d6252e7e84n%40googlegroups.com
>  
> .
> 
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>  
> .

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Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization

['David Shteynberg' via spctools-discuss]

Dear Longping,

Maybe you can compress your analysis pepXML and mzML files and post them
somewhere so I can replicate the issue locally?

Meanwhile, you can try the specifying all variable mods used in the search,
when you run PTMProphet by changing the modification string as follows:
 M:15.9949,n:42.1016,STC:299.123,C:57.02146


Cheers!

-David




On Fri, Nov 17, 2023 at 1:02 PM Longping Fu  wrote:

> I am currently working with PTMProphet in TPP version 6.3.3 for PTM
> localization. While PTMProphet successfully completes the task, I am
> encountering a significant number of warning messages in the console.
>
> To provide some context, my workflow involves utilizing MSFragger as the
> search engine to convert raw files to mzML files and then searching against
> a database. For the modification parameters, I have set M 15.9949, N-term
> 42.1016, STC 299.123, and C 57.02146 as variable modifications, with no
> fixed modifications specified.
>
> Upon obtaining the pepXML file from MSFragger, I employed Percolator for
> PSM validation using the following settings: *--only-psms --no-terminate
> --post-processing-tdc*. The resulting pepxml file was then processed with
> PTMProphet using the command: *STC:299.123 MINPROB=0.5 MODPREC=0
> FRAGPPMTOL=15 NOSTACK MAXTHREADS=1*.
>
> However, during the PTMProphet processing, I encountered warning messages
> similar to the following:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass:
> S[386]CNGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD
> (SpectraST::Peptide) = S[386]CNGGSHPR Neutral Computed Mass for Evaluation
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified
> modification masses for precision or adjust MODPREC= parameter
> ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass:
> SC[402]NGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD
> (SpectraST::Peptide) = SC[402]NGGSHPR Neutral Computed Mass for Evaluation
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified
> modification masses for precision or adjust MODPREC= parameter
> ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass:
> SCNGGS[386]HPR Neutral Mass (from pepXML) = 1254.52 BAD
> (SpectraST::Peptide) = SCNGGS[386]HPR Neutral Computed Mass for Evaluation
> = 1212.51 PPM difference = 33487.5[INFO:] please check your specified
> modification masses for precision or adjust MODPREC= parameter ...*
>
> This pattern repeats for various peptides, indicating that PTMProphet is
> struggling to localize modifications on S, T, or C. The tool suggests
> adjusting parameters, specifically the MODPREC= parameter.
>
> Has anyone encountered a similar issue with PTMProphet and successfully
> addressed it? I would greatly appreciate any insights, advice, or
> suggestions regarding this matter.
>
> --
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> 
> .
>

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Re: [spctools-discuss] XPRESS peak intensity value

['David Shteynberg' via spctools-discuss]

Hello Iryna,

The xinteract tool in the TPP, accessed in Petunia interface in [TPP Tools]
-> [Analyze peptides]) , the option -PREC can be specified in the
[PeptideProphet Options] -> [Enter additional options to pass directly to
the command-line (expert use only!)].  This option will record
precursor_intensity for each PSM in the pepXML file.  You can then add this
column in PepXMLViewer and it should be populated with parent intensities
from the mzML file.

Cheers!
-David

On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk 
wrote:

> Thank you! Do you know if there is any way to extract the precursor peak
> intensity with XPRESS (or other TPP tools)?
>
> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:
>
>> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>>
>> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk 
>> wrote:
>>
>>> Hello all!
>>> I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the
>>> "peak_intensity" output value. I was just looking to confirm whether
>>> "peak_intensity" is the precursor peak intensity, or if it's the maximum
>>> peak intensity of the ion chromatogram?
>>> Thank you
>>>
>>> --
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>>> https://groups.google.com/d/msgid/spctools-discuss/ea66065e-0b21-43cd-9f00-703ad9e8d3f7n%40googlegroups.com
>>> 
>>> .
>>>
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> 
> .
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[spctools-discuss] Re: StPeter error - Could not read spectra

[David Shteynberg]

Hey Jason,

If you are able to compress the dataset directory and share it I would be 
happy to troubleshoot this particular issue.

Cheers!
-David

On Thursday, August 31, 2023 at 12:52:42 PM UTC-7 jwi...@gmail.com wrote:

> I am trying to process my data using StPeter and am getting the following 
> error:
>
> Extracting peak intensities from 1 spectral files:
>   1 of 1: C:\TPP\data\Supernatant\PG_SS_RAW\SS1_Slot2-4_1_789.mzML   
>  0%ERROR: Could not read spectra.
>
> The data was collected on a Bruker timsTOF and converted using the 
> msconvert options "combine ion mobility scans" as well as vendor peak 
> picking and scan summing.
>
> I searched the mzML with Comet, then processed those results with 
> PeptideProphet, iProphet, and ProteinProphet. I am using TPP v6.3.3 Arcus, 
> Build 20230824-9003 (Windows_NT-x86_64). Before it crashes, StPeter 
> appears to be working:
>
> ** BEGIN StPeter ANALYSIS **
>  Time at start of analysis: Thu Aug 31 15:39:02 2023
>
>  Parameters:
>   degenerate peptides = yes
>   fdr = 0.01
>   minimum probability = 0
>   sample load = 0
>   tolerance = 0.4
>
>  Reading protXML: .\ss1_slot2-4_1_789.iproph.prot.xml
>   Probability at 0.01 FDR: 0.965
>   Number of proteins above FDR cutoff: 418
>   Number of quantifiable proteins above FDR cutoff: 418
>   Number of peptides for proteins: 822
>   Extracting true protein lengths for zero length proteins. Database: 
> uniref_taxonomy_allcombined_DECOY.fasta
>   Number of proteins fitting criteria for StPeter analysis: 418** 
> BEGIN StPeter ANALYSIS **
>  Time at start of analysis: Thu Aug 31 15:39:02 2023
>
>  Parameters:
>   degenerate peptides = yes
>   fdr = 0.01
>   minimum probability = 0
>   sample load = 0
>   tolerance = 0.4
>
>  Reading protXML: .\ss1_slot2-4_1_789.iproph.prot.xml
>   Probability at 0.01 FDR: 0.965
>   Number of proteins above FDR cutoff: 418
>   Number of quantifiable proteins above FDR cutoff: 418
>   Number of peptides for proteins: 822
>   Extracting true protein lengths for zero length proteins. Database: 
> uniref_taxonomy_allcombined_DECOY.fasta
>   Number of proteins fitting criteria for StPeter analysis: 418
>
> The mzML files are in the same directory as the protXML file, and the head 
> of the mzML appears normal:
>
> 
> http://psi.hupo.org/ms/mzml"; xmlns:xsi="
> http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="
> http://psi.hupo.org/ms/mzml 
> http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd";>
>   http://psi.hupo.org/ms/mzml"; xmlns:xsi="
> http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="
> http://psi.hupo.org/ms/mzml 
> http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd"; 
> id="SS1_Slot2-4_1_789" version="1.1.0">
> 
>   https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
>   https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo
> "/>
> 
> 
>   
>  value=""/>
>
> I also checked within the mzML file to confirm that it does contain MS2 
> scan information.
> Any advice?
>
> Jason
>

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Re: [spctools-discuss] Navigating peptideSieve Tips/Tricks?

['David Shteynberg' via spctools-discuss]

Sure!  This was my command:

[image: image.png]


On Tue, Aug 1, 2023 at 10:48 AM sophie culos  wrote:

> David, would you be at all willing to post the code that you were using?
> I'll give "/" a shot in my path definitions.
>
>
>
> On Tuesday, August 1, 2023 at 10:35:06 AM UTC-7 David Shteynberg wrote:
>
>> For what it is worth, yesterday I downloaded the PeptideSieve and ran it
>> on my system commandline to generate non-empty output files successfully.
>> I used '/' in my path definitions, but I am not sure it that makes a
>> difference.  Good luck!
>>
>> On Tue, Aug 1, 2023 at 1:21 AM 'Luis Mendoza' via spctools-discuss <
>> spctools...@googlegroups.com> wrote:
>>
>>> Hello Sophie,
>>> I don't have much help to offer at this point, since we have not used
>>> that software in a very long time.  But one thing I notice from your
>>> screenshots is that the folder/directory name appears to have a space in
>>> "MS User", which is not present in the commands, e.g.
>>> "C:\Users\msuser\TPP\...".  Perhaps this is causing the errors you observe?
>>> Cheers,
>>> --Luis
>>>
>>> On Mon, Jul 31, 2023 at 4:54 PM sophie culos  wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to use peptideSieve for an in silico digestion to identify
>>>> proteotypic peptides for MALDI.
>>>>
>>>> I've attached a screenshot of what I've been inputting into the command
>>>> line and the error I've been consistently getting. The output file is
>>>> always blank,  and I'm not sure how to proceed.
>>>>
>>>> Any help would be very much appreciated!
>>>>
>>>> Cheers,
>>>> Sophie
>>>> [image: peptideSieve error.PNG]
>>>>
>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "spctools-discuss" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to spctools-discu...@googlegroups.com.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/spctools-discuss/3017c88a-3ac5-4c9d-a8f1-34e9da686575n%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/spctools-discuss/3017c88a-3ac5-4c9d-a8f1-34e9da686575n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>> --
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>>> an email to spctools-discu...@googlegroups.com.
>>>
>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/CACyS9brV76SC0pD2K8wNwvB8xkf1dGwM2%2BCc-kgDWeOxTb89uw%40mail.gmail.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/CACyS9brV76SC0pD2K8wNwvB8xkf1dGwM2%2BCc-kgDWeOxTb89uw%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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> .
>

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Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

['David Shteynberg' via spctools-discuss]

Hi Brian,

I just confirmed in the code that it is counted here when the weight of the
peptide is minimum 0.5 and the probability minimum 0.2.

Cheers,
-David

On Wed, Jun 28, 2023 at 9:49 AM Hampton, Brian 
wrote:

> Hi David, thanks for the quick reply.
>
> I think I see now.  When there is some ambiguity which prevents
> determining a precise peptide sequence, for example incomplete fragment ion
> series, or isobaric AA assignments etc. then there must be a probability
> calculation performed, the result of which attempts to assign this peptide
> to the more likely protein candidate.  The result of which is recorded in
> the "total num peptides" value.  In the case of a tie, is the value added
> to all possible protein hits or not used?
>
> Thanks a bunch!
>
> Brian
> --
> *From:* 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com>
> *Sent:* Wednesday, June 28, 2023 12:37 PM
> *To:* spctools-discuss@googlegroups.com  >
> *Subject:* Re: [spctools-discuss] ProteinProphet output number of unique
> peptides vs total number of peptides
>
> Hello Brian,
>
> Thanks for the discussion.  The way this is possible is because there are
> degenerate peptides that map to multiple proteins, in which case only those
> that have sufficient weight will be counted as "is contributing evidence"
> peptides.  Only those PSM  instances that are contributing evidence are
> counted in the "tot num peps" value.   Please let me know if further
> clarification would be helpful or if you have other questions.
>
> Cheers,
> -David
>
> On Wed, Jun 28, 2023 at 9:27 AM Hampton, Brian 
> wrote:
>
> Hello David,
>
> I have difficulty understanding this.  I had always operated under the
> assumption that the "num unique peps" would be less than or equal to the
> "tot num peps" - because - I thought "tot num peps" = "num unique peps" +
> number of (shared) peptides also mapping to given protein.  Is this not the
> case and if so how would "tot num peps" ever be less than "num unique peps"?
>
> Best regards,
> Brian
>
>
>
> Brian Hampton
> Proteomics Core Lab
>
> Center for Vascular and Inflammatory Diseases
>
> University of Maryland School of Medicine
>
> BioPark One Rm 307
>
> 800 West Baltimore Street
>
> Baltimore, MD. 21201
>
> (410)706-8207
> --
> *From:* 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com>
> *Sent:* Wednesday, June 28, 2023 11:33 AM
> *To:* spctools-discuss@googlegroups.com  >
> *Subject:* Re: [spctools-discuss] ProteinProphet output number of unique
> peptides vs total number of peptides
>
> Hi Murielle,
>
> Sorry this is a little confusing.  Column "num unique peps" represents
> total number of unique peptides mapping to the protein.  The "tot num peps"
> counts the PSMs that are "contributing evidence" (last column) to the
> protein, sometimes this number can be lower because not all peptides
> mapping are contributing evidence and spectral counts can be low per
> peptide.
>
> The answer to your second question is *yes*, the "tot num peps" is the
> spectral count for "is contributing evidence" peptides.
>
> Cheers,
> -David
>
>
> On Wed, Jun 28, 2023 at 7:27 AM muriell...@gmail.com <
> murielle.al...@gmail.com> wrote:
>
> Hi David,
>
> Thank you for such a quick reply!
>
> I used tpp version 6.2.0 run via a singularity image and I produced the
> table by including the EXCELXX option in proteinprophet.
>
> Cheers,
>
> Murielle
>
> On Wednesday, June 28, 2023 at 12:44:03 AM UTC+2 David Shteynberg wrote:
>
> Hi Murielle,
>
> Thanks for using the TPP and submitting your question here.   When I try
> the latest version of the TPP and run ProteinProphet through there, the
> columns exported in my tab separated file from ProteinProphet are different
> from yours.  Can you please provide a bit more information about how you
> generated this file and which version of the software you used?
>
> Cheers,
> -David
>
> On Tue, Jun 27, 2023 at 7:10 AM muriell...@gmail.com 
> wrote:
>
> Hi all,
>
> I have two questions concerning the output of ProteinProphet :
>
> 1) Why do I have some entries for which the total number of peptides is
> lower than the number of unique peptides?  (see columns 5 and 6 below, an
> extract of my output table)
>
> [image: protein prophet output.jpeg]
> 2) Does the column "total number of peptides" correspond to spectral
> c

Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

['David Shteynberg' via spctools-discuss]

Hi Emma,

Yes, for spectral counting of proteins it seems appropriate to consider
only "is contributing evidence" peptides,  "tot num peps"  would be the
value to use.

Cheers,
-David

On Wed, Jun 28, 2023 at 9:35 AM Emma Whittington  wrote:

> I am also a little confused/requiring clarification. For label-free
> quantification would you use the "tot num peps" for spectral counts when
> calculating something like NSAF? From your description, it sounds like
> that's the total number of contributing spectra.
>
> all the best,
> Emma
> On Wednesday, 28 June 2023 at 18:27:48 UTC+2 Hampton, Brian wrote:
>
>> Hello David,
>>
>> I have difficulty understanding this.  I had always operated under the
>> assumption that the "num unique peps" would be less than or equal to the
>> "tot num peps" - because - I thought "tot num peps" = "num unique peps" +
>> number of (shared) peptides also mapping to given protein.  Is this not the
>> case and if so how would "tot num peps" ever be less than "num unique peps"?
>>
>> Best regards,
>> Brian
>>
>>
>>
>> Brian Hampton
>> Proteomics Core Lab
>>
>> Center for Vascular and Inflammatory Diseases
>>
>> University of Maryland School of Medicine
>>
>> BioPark One Rm 307
>>
>> 800 West Baltimore Street
>>
>> Baltimore, MD. 21201
>>
>> (410)706-8207 <(410)%20706-8207>
>> --
>> *From:* 'David Shteynberg' via spctools-discuss <
>> spctools...@googlegroups.com>
>> *Sent:* Wednesday, June 28, 2023 11:33 AM
>> *To:* spctools...@googlegroups.com 
>> *Subject:* Re: [spctools-discuss] ProteinProphet output number of unique
>> peptides vs total number of peptides
>>
>> Hi Murielle,
>>
>> Sorry this is a little confusing.  Column "num unique peps" represents
>> total number of unique peptides mapping to the protein.  The "tot num peps"
>> counts the PSMs that are "contributing evidence" (last column) to the
>> protein, sometimes this number can be lower because not all peptides
>> mapping are contributing evidence and spectral counts can be low per
>> peptide.
>>
>> The answer to your second question is *yes*, the "tot num peps" is the
>> spectral count for "is contributing evidence" peptides.
>>
>> Cheers,
>> -David
>>
>>
>> On Wed, Jun 28, 2023 at 7:27 AM muriell...@gmail.com <
>> muriell...@gmail.com> wrote:
>>
>> Hi David,
>>
>> Thank you for such a quick reply!
>>
>> I used tpp version 6.2.0 run via a singularity image and I produced the
>> table by including the EXCELXX option in proteinprophet.
>>
>> Cheers,
>>
>> Murielle
>>
>> On Wednesday, June 28, 2023 at 12:44:03 AM UTC+2 David Shteynberg wrote:
>>
>> Hi Murielle,
>>
>> Thanks for using the TPP and submitting your question here.   When I try
>> the latest version of the TPP and run ProteinProphet through there, the
>> columns exported in my tab separated file from ProteinProphet are different
>> from yours.  Can you please provide a bit more information about how you
>> generated this file and which version of the software you used?
>>
>> Cheers,
>> -David
>>
>> On Tue, Jun 27, 2023 at 7:10 AM muriell...@gmail.com <
>> muriell...@gmail.com> wrote:
>>
>> Hi all,
>>
>> I have two questions concerning the output of ProteinProphet :
>>
>> 1) Why do I have some entries for which the total number of peptides is
>> lower than the number of unique peptides?  (see columns 5 and 6 below, an
>> extract of my output table)
>>
>> [image: protein prophet output.jpeg]
>> 2) Does the column "total number of peptides" correspond to spectral
>> counts?
>>
>> Thank you very much ,
>>
>> Murielle
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to spctools-discu...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/be3b35c9-e308-4e35-8551-03425f7d1704n%40googlegroups.com
>> <https://groups.google.com/d/msgid/spctools-discuss/be3b35c9-e308-4e35-8551-03425f7d1704n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>> --

Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

['David Shteynberg' via spctools-discuss]

Hello Brian,

Thanks for the discussion.  The way this is possible is because there are
degenerate peptides that map to multiple proteins, in which case only those
that have sufficient weight will be counted as "is contributing evidence"
peptides.  Only those PSM  instances that are contributing evidence are
counted in the "tot num peps" value.   Please let me know if further
clarification would be helpful or if you have other questions.

Cheers,
-David

On Wed, Jun 28, 2023 at 9:27 AM Hampton, Brian 
wrote:

> Hello David,
>
> I have difficulty understanding this.  I had always operated under the
> assumption that the "num unique peps" would be less than or equal to the
> "tot num peps" - because - I thought "tot num peps" = "num unique peps" +
> number of (shared) peptides also mapping to given protein.  Is this not the
> case and if so how would "tot num peps" ever be less than "num unique peps"?
>
> Best regards,
> Brian
>
>
>
> Brian Hampton
> Proteomics Core Lab
>
> Center for Vascular and Inflammatory Diseases
>
> University of Maryland School of Medicine
>
> BioPark One Rm 307
>
> 800 West Baltimore Street
>
> Baltimore, MD. 21201
>
> (410)706-8207
> --
> *From:* 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com>
> *Sent:* Wednesday, June 28, 2023 11:33 AM
> *To:* spctools-discuss@googlegroups.com  >
> *Subject:* Re: [spctools-discuss] ProteinProphet output number of unique
> peptides vs total number of peptides
>
> Hi Murielle,
>
> Sorry this is a little confusing.  Column "num unique peps" represents
> total number of unique peptides mapping to the protein.  The "tot num peps"
> counts the PSMs that are "contributing evidence" (last column) to the
> protein, sometimes this number can be lower because not all peptides
> mapping are contributing evidence and spectral counts can be low per
> peptide.
>
> The answer to your second question is *yes*, the "tot num peps" is the
> spectral count for "is contributing evidence" peptides.
>
> Cheers,
> -David
>
>
> On Wed, Jun 28, 2023 at 7:27 AM muriell...@gmail.com <
> murielle.al...@gmail.com> wrote:
>
> Hi David,
>
> Thank you for such a quick reply!
>
> I used tpp version 6.2.0 run via a singularity image and I produced the
> table by including the EXCELXX option in proteinprophet.
>
> Cheers,
>
> Murielle
>
> On Wednesday, June 28, 2023 at 12:44:03 AM UTC+2 David Shteynberg wrote:
>
> Hi Murielle,
>
> Thanks for using the TPP and submitting your question here.   When I try
> the latest version of the TPP and run ProteinProphet through there, the
> columns exported in my tab separated file from ProteinProphet are different
> from yours.  Can you please provide a bit more information about how you
> generated this file and which version of the software you used?
>
> Cheers,
> -David
>
> On Tue, Jun 27, 2023 at 7:10 AM muriell...@gmail.com 
> wrote:
>
> Hi all,
>
> I have two questions concerning the output of ProteinProphet :
>
> 1) Why do I have some entries for which the total number of peptides is
> lower than the number of unique peptides?  (see columns 5 and 6 below, an
> extract of my output table)
>
> [image: protein prophet output.jpeg]
> 2) Does the column "total number of peptides" correspond to spectral
> counts?
>
> Thank you very much ,
>
> Murielle
>
> --
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Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides

['David Shteynberg' via spctools-discuss]

Hi Murielle,

Sorry this is a little confusing.  Column "num unique peps" represents
total number of unique peptides mapping to the protein.  The "tot num peps"
counts the PSMs that are "contributing evidence" (last column) to the
protein, sometimes this number can be lower because not all peptides
mapping are contributing evidence and spectral counts can be low per
peptide.

The answer to your second question is *yes*, the "tot num peps" is the
spectral count for "is contributing evidence" peptides.

Cheers,
-David


On Wed, Jun 28, 2023 at 7:27 AM muriell...@gmail.com <
murielle.al...@gmail.com> wrote:

> Hi David,
>
> Thank you for such a quick reply!
>
> I used tpp version 6.2.0 run via a singularity image and I produced the
> table by including the EXCELXX option in proteinprophet.
>
> Cheers,
>
> Murielle
>
> On Wednesday, June 28, 2023 at 12:44:03 AM UTC+2 David Shteynberg wrote:
>
>> Hi Murielle,
>>
>> Thanks for using the TPP and submitting your question here.   When I try
>> the latest version of the TPP and run ProteinProphet through there, the
>> columns exported in my tab separated file from ProteinProphet are different
>> from yours.  Can you please provide a bit more information about how you
>> generated this file and which version of the software you used?
>>
>> Cheers,
>> -David
>>
>> On Tue, Jun 27, 2023 at 7:10 AM muriell...@gmail.com <
>> muriell...@gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> I have two questions concerning the output of ProteinProphet :
>>>
>>> 1) Why do I have some entries for which the total number of peptides is
>>> lower than the number of unique peptides?  (see columns 5 and 6 below, an
>>> extract of my output table)
>>>
>>> [image: protein prophet output.jpeg]
>>> 2) Does the column "total number of peptides" correspond to spectral
>>> counts?
>>>
>>> Thank you very much ,
>>>
>>> Murielle
>>>
>>> --
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>>> .
>>>
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Re: [spctools-discuss] Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022

['David Shteynberg' via spctools-discuss]

Hello Scott,

You should be able to get around this issue by unchecking the option to
download and install Kojak dependencies during the installation.  If that
still fails let me know.

Cheers,
-David

On Thu, May 4, 2023 at 9:31 PM Scott Starry  wrote:

> Due to security restrictions, my company does not allow redirected calls,
> which the TPP 6.3.0 installer uses to obtain the Microsoft Visual C++
> redistributables.  This is usually not a problem as I simply install the MS
> VC++ 2010 and 2015-2022 redistributables beforehand.
>
> v5.2.0 found the two redistributables and did not attempt to install
> them.  However, TPP v6.3.0 only recognizes that the 2010 redistributable is
> already installed; the installer tries to install the 2015-2022
> redistributable causing the the Windows installer to crash in my
> environment.
>
> Would be good if the v6.3.0 installer would recognize that both
> prerequisites are already installed.
>
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Re: [spctools-discuss] protein prophet failing on Eclipse searches

['David Shteynberg' via spctools-discuss]

Hello,

Generally this message means that you have no PSMs with good likelihoods of
being correct in this analysis set.
There are a few "usual suspect" reasons for why you would not observe any
PSMs with non-zero probabilities among your results.

1. Poor quality data (e.g. empty sample)

2. Incorrect database (e.g. wrong organism, common contaminants missing)

3. Incorrect search parameters (e.g. wrong tolerances or incorrect static
modifications specified)

Please go down the list to help yourself troubleshoot.

-David





On Tue, Nov 29, 2022 at 4:34 PM 'Luis Mendoza' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> Hi,
> Congrats on the new instrument, and happy holidays as well!
>
> The error seems to indicate that there is no input data for ProteinProphet
> to work with; can you verify that the input file contains validated search
> results with probabilities above 0.2 ?  Are there any other errors or
> warnings in the previous steps?
>
> Feel free to directly send me the interact.pep.xml file and I can have a
> look as well.
>
> Cheers,
> --Luis
>
>
> On Tue, Nov 29, 2022 at 10:31 AM cabarnes...@gmail.com <
> cabarnescabar...@gmail.com> wrote:
>
>> Hi all,
>>
>> Happy holidays!  I have a new Eclipse in the lab and have been running my
>> Comet + TPP pipeline successfully on a lot of data downloaded from PRIDE
>> lately, but have run into an error with the new DDA data generated on the
>> Eclipse.  It seems to be failing at the protein prophet step and the error
>> doesn't make much sense to me.  Any idea what is going on?
>>
>> I'm running TPP 6.1 and Comet 2022.01 rev. 1 although the error below is
>> from the output of the Comet search through the TPP interface.  I get a
>> similar error on the command line at the same step.
>>
>>
>> Here's the error message:
>>
>> WARNING: no data - output file will be empty
>>
>> command "C:/TPP/bin/ProteinProphet "interact.pep.xml"
>> "interact.prot.xml"" failed: Operation not permitted
>>
>> command "C:/TPP/bin/ProteinProphet "interact.pep.xml"
>> "interact.prot.xml"" exited with non-zero exit code: 1
>> QUIT - the job is incomplete
>>
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>> 
>> .
>>
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Re: [spctools-discuss] Error running xinteract on Kojak results using latest Docker image

['David Shteynberg' via spctools-discuss]

Hi Mike,

With Kojak data the peptide length is meaningless and recorded as zero in
the pepXML.  The default parameters of xinteract use min peptide length of
7 which invalidates all results in this file.  You have to run with min
peptide length of zero when processing Kojak data: xinteract -l0

Cheers!
-David

On Mon, Nov 14, 2022 at 5:06 PM Michael Riffle  wrote:

> Greetings TPP folks,
>
> I just pulled the latest Docker image and am trying to run the Kojak then
> PeptideProphet. Kojak runs fine, PeptideProphet produces an error. Here is
> my output:
>
> ```
> sudo docker run -v `pwd`:/data spctools/tpp xinteract
> QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml
>
> xinteract (TPP v6.1.0 Parhelion, Build 202206071715-8676 (Linux-x86_64))
>
> running: "/usr/local/tpp/bin/InteractParser 'interact.pep.xml'
> 'QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml' -L'7'"
>  file 1: QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml
>  processed altogether 77134 results
> INFO: Results written to file: /data/interact.pep.xml
> command completed in 5 sec
>
> running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'"
> command completed in 1 sec
>
> running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml'
> '/data/EH217_3pepCnt_plusRev.fasta'"
> enzyme name is:trypsin
>   - Building Commentz-Walter keyword tree...
>   - Searching the tree...
>   - Linking duplicate entries...
>   - Printing results...
>   - Mapped 42490 entries
>
> command completed in 3 sec
>  using MAXEHFX_2019_0510_AZ_034_eh220_comet.pep.xml for PeptideProphet...
>
> running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'"
>  (Kojak)
> init with Kojak trypsin
> init Loop model with Kojak trypsin
> adding XLSecondScoreFraction mixture distribution
> adding XLTopExpectScore mixture distribution
> init XL model with Kojak trypsin
>  PeptideProphet  (TPP v6.1.0 Parhelion, Build 202206071715-8676
> (Linux-x86_64)) AKeller@ISB
>  read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
>  read in no data
> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>
> INFO: Processing xl MixtureModel ...
>
> command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'"
> exited with non-zero exit code: 256
> QUIT - the job is incomplete
> ```
>
> I suspect the "read no data" line above, towards the end, is the culprit,
> but I can't guess what might be causing that. Do you have any ideas?
>
> Thanks,
> Mike Riffle
>
>
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Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

['David Shteynberg' via spctools-discuss]

I am unable to reproduce this error when I download and run the tutorial on
my windows or linux (ubuntu) machines with this tutorial data.  Perhaps you
can confirm that the fasta file you have is not getting corrupted somehow
during your download or processing.  Thanks.

-David

On Fri, Jun 10, 2022 at 1:37 PM Malcolm Cook  wrote:

> I discovered the issue.  I believe you have a bug.
>
> In my hands, when the fasta deflines in Yeast_UPS_cRAP.fasta are longer
> than 120 characters they get truncated and a non-breaking space appended.
>
> Running the demo pipeline runs to completion if I first fix this problem
> with:
>
>
> *sudo -u apache bash -c 'perl -pi -e "s|^(>.{119,119})(.*)\$|\$1|"
>  /data/tpp/tests/QuickYeastUPS1/Yeast_UPS_cRAP.fasta'*
>
>
> On Friday, June 10, 2022 at 1:14:08 PM UTC-5 Malcolm Cook wrote:
>
>> Thank you.  I concur deleting those characters resolves the issue.
>>
>> My colleague Gabriel actually was running the tutorial test.  I will ask
>> him to chime in if he did anything other than follow the steps given.
>>
>> On Friday, June 10, 2022 at 12:03:08 PM UTC-5 David Shteynberg wrote:
>>
>>> Hello again Malcolm,
>>>
>>> There are several of these non-ascii characters in the protXML file that
>>> you sent.  After I removed them I was able to open the file in
>>> ProtXMLViewer.  Also the syntax errors from tpp2mzid went away (although I
>>> wasn't able to convert your file without the associated pepXML data.)
>>>  Please let us know if you are able to resolve this issue on your end.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Fri, Jun 10, 2022 at 7:35 AM Malcolm Cook 
>>> wrote:
>>>
>>>> I just got TPP installed and am trying to [test the installation with a
>>>> sample dataset](
>>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS#Testing_the_installation_with_a_sample_dataset_.28optional.29
>>>> )
>>>>
>>>> I am getting an error with tpp2mzid parsing ProteinProphet output (here
>>>> is the full file
>>>> <https://ftp.stowers.org/public/mec/tpp/interact.prot.xml>).
>>>>
>>>> Reviewing the ISB/SPC Trans Proteomic Pipeline :: Jobs logs I read our
>>>> ProteinProphet completed with success:
>>>>
>>>>
>>>> *Finished. Results written to:
>>>> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlhowever *
>>>> however trying to process it with tpp2mzid gives error
>>>>
>>>>
>>>>
>>>>
>>>> *Reading:
>>>> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148)
>>>> : error 4: Syntax error parsing XML.Failed to read protXML:
>>>> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlmanually *
>>>> inspecting this file it looks like a well formed big ball of XML to my
>>>> eyes:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *>>> href="http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl
>>>> <http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl>"?>>>> xmlns="http://regis-web.systemsbiology.net/protXML
>>>> <http://regis-web.systemsbiology.net/protXML>"
>>>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance
>>>> <http://www.w3.org/2001/XMLSchema-instance>"
>>>> xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd
>>>> <http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd>"
>>>> summary_xml="/data/tpp/tests/QuickYeastUPS1/interact.prot.xml">>>> reference_database="/data/tpp/tests/QuickYeastUPS1/Yeast_UPS_cRAP.fasta"
>>>> residue_substitution_list="I -> L"
>>>> source_files="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
>>>> source_files_alt="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
>>>> min_peptide_probability="0.20" min_peptide_weight="0.50"
>>>> num_predicted_correct_prots="98.6" num_input_1_spectra="0"
>>>> num_input_2_spectra="348" num_input_3_spectra="70" num_input_4_spectra="0"
>>>> n

Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

['David Shteynberg' via spctools-discuss]

Which specific tutorial are you attempting so I can try to reproduce
the issue?

Thanks,
-David



On Fri, Jun 10, 2022 at 11:14 AM Malcolm Cook 
wrote:

> Thank you.  I concur deleting those characters resolves the issue.
>
> My colleague Gabriel actually was running the tutorial test.  I will ask
> him to chime in if he did anything other than follow the steps given.
>
> On Friday, June 10, 2022 at 12:03:08 PM UTC-5 David Shteynberg wrote:
>
>> Hello again Malcolm,
>>
>> There are several of these non-ascii characters in the protXML file that
>> you sent.  After I removed them I was able to open the file in
>> ProtXMLViewer.  Also the syntax errors from tpp2mzid went away (although I
>> wasn't able to convert your file without the associated pepXML data.)
>>  Please let us know if you are able to resolve this issue on your end.
>>
>> Cheers,
>> -David
>>
>> On Fri, Jun 10, 2022 at 7:35 AM Malcolm Cook  wrote:
>>
>>> I just got TPP installed and am trying to [test the installation with a
>>> sample dataset](
>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS#Testing_the_installation_with_a_sample_dataset_.28optional.29
>>> )
>>>
>>> I am getting an error with tpp2mzid parsing ProteinProphet output (here
>>> is the full file
>>> <https://ftp.stowers.org/public/mec/tpp/interact.prot.xml>).
>>>
>>> Reviewing the ISB/SPC Trans Proteomic Pipeline :: Jobs logs I read our
>>> ProteinProphet completed with success:
>>>
>>>
>>> *Finished. Results written to:
>>> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlhowever *
>>> however trying to process it with tpp2mzid gives error
>>>
>>>
>>>
>>>
>>> *Reading:
>>> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148)
>>> : error 4: Syntax error parsing XML.Failed to read protXML:
>>> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlmanually *
>>> inspecting this file it looks like a well formed big ball of XML to my
>>> eyes:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *>> href="http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl
>>> <http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl>"?>>> xmlns="http://regis-web.systemsbiology.net/protXML
>>> <http://regis-web.systemsbiology.net/protXML>"
>>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance
>>> <http://www.w3.org/2001/XMLSchema-instance>"
>>> xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd
>>> <http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd>"
>>> summary_xml="/data/tpp/tests/QuickYeastUPS1/interact.prot.xml">>> reference_database="/data/tpp/tests/QuickYeastUPS1/Yeast_UPS_cRAP.fasta"
>>> residue_substitution_list="I -> L"
>>> source_files="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
>>> source_files_alt="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
>>> min_peptide_probability="0.20" min_peptide_weight="0.50"
>>> num_predicted_correct_prots="98.6" num_input_1_spectra="0"
>>> num_input_2_spectra="348" num_input_3_spectra="70" num_input_4_spectra="0"
>>> num_input_5_spectra="0" initial_min_peptide_prob="0.05"
>>> total_no_spectrum_ids="357.6" sample_enzyme="trypsin">>> analysis="proteinprophet" time="2022-06-09T09:15:57" version="
>>> Insilicos_LabKey_C++ (TPP v6.1.0 Parhelion, Build 202206081159-exported
>>> (Linux-x86_64))">>> degen_flag="Y" nsp_flag="Y" fpkm_flag="N" initial_peptide_wt_iters="2"
>>> nsp_distribution_iters="3" final_peptide_wt_iters="0"
>>> run_options="IPROPHET"> >> neighboring_bin_smoothing="Y">...*
>>> trying to run  tpp2mzid  from the command line sheds little light:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> */usr/local/tpp/bin/tpp2mzid
>>> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmltpp2mzid v0.9.11 (May 19
>>> 2022), copyright Mike Hoopmann, Institute for Syste

Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

['David Shteynberg' via spctools-discuss]

Hello again Malcolm,

There are several of these non-ascii characters in the protXML file that
you sent.  After I removed them I was able to open the file in
ProtXMLViewer.  Also the syntax errors from tpp2mzid went away (although I
wasn't able to convert your file without the associated pepXML data.)
 Please let us know if you are able to resolve this issue on your end.

Cheers,
-David

On Fri, Jun 10, 2022 at 7:35 AM Malcolm Cook  wrote:

> I just got TPP installed and am trying to [test the installation with a
> sample dataset](
> http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS#Testing_the_installation_with_a_sample_dataset_.28optional.29
> )
>
> I am getting an error with tpp2mzid parsing ProteinProphet output (here
> is the full file
> ).
>
> Reviewing the ISB/SPC Trans Proteomic Pipeline :: Jobs logs I read our
> ProteinProphet completed with success:
>
>
> *Finished. Results written to:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlhowever *
> however trying to process it with tpp2mzid gives error
>
>
>
>
> *Reading:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148)
> : error 4: Syntax error parsing XML.Failed to read protXML:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlmanually *
> inspecting this file it looks like a well formed big ball of XML to my
> eyes:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> * href="http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl
> "?> xmlns="http://regis-web.systemsbiology.net/protXML
> "
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance
> "
> xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd
> "
> summary_xml="/data/tpp/tests/QuickYeastUPS1/interact.prot.xml"> reference_database="/data/tpp/tests/QuickYeastUPS1/Yeast_UPS_cRAP.fasta"
> residue_substitution_list="I -> L"
> source_files="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
> source_files_alt="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
> min_peptide_probability="0.20" min_peptide_weight="0.50"
> num_predicted_correct_prots="98.6" num_input_1_spectra="0"
> num_input_2_spectra="348" num_input_3_spectra="70" num_input_4_spectra="0"
> num_input_5_spectra="0" initial_min_peptide_prob="0.05"
> total_no_spectrum_ids="357.6" sample_enzyme="trypsin"> analysis="proteinprophet" time="2022-06-09T09:15:57" version="
> Insilicos_LabKey_C++ (TPP v6.1.0 Parhelion, Build 202206081159-exported
> (Linux-x86_64))"> degen_flag="Y" nsp_flag="Y" fpkm_flag="N" initial_peptide_wt_iters="2"
> nsp_distribution_iters="3" final_peptide_wt_iters="0"
> run_options="IPROPHET">  neighboring_bin_smoothing="Y">...*
> trying to run  tpp2mzid  from the command line sheds little light:
>
>
>
>
>
>
>
>
> */usr/local/tpp/bin/tpp2mzid
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmltpp2mzid v0.9.11 (May 19
> 2022), copyright Mike Hoopmann, Institute for Systems Biology.Built using
> mzIMLTools: 1.2.6Mar 21 2022Built using NeoPepXMLParser: 1.0.22022
> MAY 17Built using NeoProtXMLParser: 1.0.02022 MAY 19Reading:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148)
> : error 4: Syntax error parsing XML.Failed to read protXML:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml*
> how to diagnose/debug/fix?
>
> Thanks!
>
> --
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> 
> .
>

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Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML

['David Shteynberg' via spctools-discuss]

Hi Malcolm,

The message is complaining about line 148 of the pepXML file which look
like this:



Apparently this protein entry in your database has a non-ascii character in
the descriptions of this protein.  Can you please share this database so I
can examine this protein entry or can you check it in the fasta file?  I
think the problem might be somewhere upstream of the error but would need
to do a bit more digging to confirm.  Also if you are able, please compress
and share the data from the whole analysis you've done so I can trace where
the failure occurs.

Thanks!
-David

On Fri, Jun 10, 2022 at 7:35 AM Malcolm Cook  wrote:

> I just got TPP installed and am trying to [test the installation with a
> sample dataset](
> http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS#Testing_the_installation_with_a_sample_dataset_.28optional.29
> )
>
> I am getting an error with tpp2mzid parsing ProteinProphet output (here
> is the full file
> ).
>
> Reviewing the ISB/SPC Trans Proteomic Pipeline :: Jobs logs I read our
> ProteinProphet completed with success:
>
>
> *Finished. Results written to:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlhowever *
> however trying to process it with tpp2mzid gives error
>
>
>
>
> *Reading:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148)
> : error 4: Syntax error parsing XML.Failed to read protXML:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmlmanually *
> inspecting this file it looks like a well formed big ball of XML to my
> eyes:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> * href="http://hd1991356yb/tests/QuickYeastUPS1/interact.prot.xsl
> "?> xmlns="http://regis-web.systemsbiology.net/protXML
> "
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance
> "
> xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v9.xsd
> "
> summary_xml="/data/tpp/tests/QuickYeastUPS1/interact.prot.xml"> reference_database="/data/tpp/tests/QuickYeastUPS1/Yeast_UPS_cRAP.fasta"
> residue_substitution_list="I -> L"
> source_files="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
> source_files_alt="/data/tpp/tests/QuickYeastUPS1/interact.ipro.pep.xml"
> min_peptide_probability="0.20" min_peptide_weight="0.50"
> num_predicted_correct_prots="98.6" num_input_1_spectra="0"
> num_input_2_spectra="348" num_input_3_spectra="70" num_input_4_spectra="0"
> num_input_5_spectra="0" initial_min_peptide_prob="0.05"
> total_no_spectrum_ids="357.6" sample_enzyme="trypsin"> analysis="proteinprophet" time="2022-06-09T09:15:57" version="
> Insilicos_LabKey_C++ (TPP v6.1.0 Parhelion, Build 202206081159-exported
> (Linux-x86_64))"> degen_flag="Y" nsp_flag="Y" fpkm_flag="N" initial_peptide_wt_iters="2"
> nsp_distribution_iters="3" final_peptide_wt_iters="0"
> run_options="IPROPHET">  neighboring_bin_smoothing="Y">...*
> trying to run  tpp2mzid  from the command line sheds little light:
>
>
>
>
>
>
>
>
> */usr/local/tpp/bin/tpp2mzid
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xmltpp2mzid v0.9.11 (May 19
> 2022), copyright Mike Hoopmann, Institute for Systems Biology.Built using
> mzIMLTools: 1.2.6Mar 21 2022Built using NeoPepXMLParser: 1.0.22022
> MAY 17Built using NeoProtXMLParser: 1.0.02022 MAY 19Reading:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml/data/tpp/tests/QuickYeastUPS1/interact.prot.xml(148)
> : error 4: Syntax error parsing XML.Failed to read protXML:
> /data/tpp/tests/QuickYeastUPS1/interact.prot.xml*
> how to diagnose/debug/fix?
>
> Thanks!
>
> --
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> 
> .
>

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Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl

['David Shteynberg' via spctools-discuss]

Great! Thank you for keep and sharing your useful notes in this process.
Let us know if you encounter other issues or have any questions.

Cheers,
David

On Wed, Jun 8, 2022, 5:37 PM Malcolm Cook  wrote:

> Things I've tried and failed (with an `apachectl restart` after each)
>
>1.  sudo chown -R apache.apache /usr/local/tpp/cgi-bin;
>2.  sudo chown -R apache.apache /usr/local/tpp
>3.
>4.  sudo chmod 755 -R apache.apache /usr/local/tpp
>5. disabled other /etc/httpd/conf.d/
>
> FIXED!  There was interference from another app being served (incorrectly)
> on this server.
>
> Mea culpa,
>
> ~ Malcolm
> On Wednesday, June 8, 2022 at 5:17:49 PM UTC-5 Malcolm Cook wrote:
>
>> an oddity re: the error message is it says " ExecCGI is off in this
>> directory: /usr/local/tpp/cgi-bin/tpp_gui.pl"  but it names a file, not
>> a directory.
>>
>> ...maybe nothing.
>>
>> On Wednesday, June 8, 2022 at 5:14:17 PM UTC-5 Malcolm Cook wrote:
>>
>>> hi again
>>> yes, I reported the only entry after fresh restart of apache and
>>> accessing that url I get the following in the error log:
>>>
>>> [Wed Jun 08 17:08:31.331141 2022] [mpm_prefork:notice] [pid 4451]
>>> AH00163: Apache/2.4.6 (CentOS) configured -- resuming normal operations
>>> [Wed Jun 08 17:08:31.331189 2022] [core:notice] [pid 4451] AH00094:
>>> Command line: '/usr/sbin/httpd -D FOREGROUND'
>>> [Wed Jun 08 17:08:39.167358 2022] [cgi:error] [pid 4453] [client
>>> 127.0.0.1:44684] Options ExecCGI is off in this directory:
>>> /usr/local/tpp/cgi-bin/tpp_gui.pl
>>>
>>> corresponding to this in the access log:
>>>
>>> 127.0.0.1 - - [08/Jun/2022:17:08:39 -0500] "GET /tpp/cgi-bin/tpp_gui.pl
>>> HTTP/1.1" 403 224 "-" "Mozilla/5.0 (X11; Linux x86_64; rv:91.0)
>>> Gecko/20100101 Firefox/91.0"
>>>
>>> On Wednesday, June 8, 2022 at 5:04:27 PM UTC-5 David Shteynberg wrote:
>>>
>>>> It sounds like you are making progress get this installed and running.
>>>> Can you check the apache error logs to see if they hold the next clue?
>>>>
>>>> Thanks,
>>>> David
>>>>
>>>> On Wed, Jun 8, 2022, 4:25 PM Malcolm Cook  wrote:
>>>>
>>>>> I just finished building and installing TPP under centos7
>>>>>
>>>>> Following Testing the installation with a sample dataset
>>>>> <http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS#Testing_the_installation_with_a_sample_dataset_.28optional.29>
>>>>>  on
>>>>> I navigate to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
>>>>>
>>>>> I am running apache as user 'apache'
>>>>>
>>>>> It returns 403/Forbidden
>>>>>
>>>>> I think I must have some permissions/ownership wrong somewhere
>>>>>
>>>>> The error log shows:
>>>>>
>>>>>  Options ExecCGI is off in this directory: /usr/local/tpp/cgi-bin/
>>>>> tpp_gui.pl
>>>>>
>>>>> This should not be since the installed httpd-2.4-tpp-1.conf indeed has
>>>>> this stanza:
>>>>>
>>>>> Alias //tpp/cgi-bin "/usr/local/tpp/cgi-bin"
>>>>> 
>>>>> Options MultiViews ExecCGI
>>>>> AddHandler cgi-script .pl .cgi
>>>>> ...
>>>>>
>>>>> Any ideas?
>>>>>
>>>>> Here are some more configuration diagnostics that might help...
>>>>>
>>>>> the CGI program is executable by anyone and owned by user tpp:
>>>>>
>>>>> ls -la /usr/local/tpp/cgi-bin/tpp_gui.pl
>>>>> -r-xr-xr-x 1 tpp tpp 484152 Jun  8 14:19 /usr/local/tpp/cgi-bin/
>>>>> tpp_gui.pl
>>>>>
>>>>> Below I review the ownership of directories within /usr/local/tpp
>>>>>
>>>>>  tree -u -d /usr/local/tpp
>>>>> /usr/local/tpp
>>>>> |-- [tpp ]  bin
>>>>> |-- [tpp ]  cgi-bin
>>>>> |-- [tpp ]  conf
>>>>> |-- [tpp ]  html
>>>>> |   |-- [tpp ]  css
>>>>> |   |-- [tpp ]  images
>>>>> |   |   |-- [tpp ]  help
>>>>> |   |   `-- [tpp ]  lorikeet
>>>>> |   |-- [tpp ]  js
>>>>> |   `-- [tpp ]

Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl

['David Shteynberg' via spctools-discuss]

It sounds like you are making progress get this installed and running. Can
you check the apache error logs to see if they hold the next clue?

Thanks,
David

On Wed, Jun 8, 2022, 4:25 PM Malcolm Cook  wrote:

> I just finished building and installing TPP under centos7
>
> Following Testing the installation with a sample dataset
> 
>  on
> I navigate to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
>
> I am running apache as user 'apache'
>
> It returns 403/Forbidden
>
> I think I must have some permissions/ownership wrong somewhere
>
> The error log shows:
>
>  Options ExecCGI is off in this directory: /usr/local/tpp/cgi-bin/
> tpp_gui.pl
>
> This should not be since the installed httpd-2.4-tpp-1.conf indeed has
> this stanza:
>
> Alias //tpp/cgi-bin "/usr/local/tpp/cgi-bin"
> 
> Options MultiViews ExecCGI
> AddHandler cgi-script .pl .cgi
> ...
>
> Any ideas?
>
> Here are some more configuration diagnostics that might help...
>
> the CGI program is executable by anyone and owned by user tpp:
>
> ls -la /usr/local/tpp/cgi-bin/tpp_gui.pl
> -r-xr-xr-x 1 tpp tpp 484152 Jun  8 14:19 /usr/local/tpp/cgi-bin/tpp_gui.pl
>
> Below I review the ownership of directories within /usr/local/tpp
>
>  tree -u -d /usr/local/tpp
> /usr/local/tpp
> |-- [tpp ]  bin
> |-- [tpp ]  cgi-bin
> |-- [tpp ]  conf
> |-- [tpp ]  html
> |   |-- [tpp ]  css
> |   |-- [tpp ]  images
> |   |   |-- [tpp ]  help
> |   |   `-- [tpp ]  lorikeet
> |   |-- [tpp ]  js
> |   `-- [tpp ]  ref
> |-- [tpp ]  lib
> |   |-- [tpp ]  Mayu
> |   |   `-- [tpp ]  R
> |   `-- [tpp ]  perl
> |   `-- [tpp ]  TPP
> |-- [tpp ]  lic
> |   |-- [tpp ]  ProteoWizard
> |   |-- [tpp ]  boost
> |   |-- [tpp ]  bzip2
> |   |-- [tpp ]  d3
> |   |-- [tpp ]  expat
> |   |-- [tpp ]  fann
> |   |-- [tpp ]  gsl
> |   |-- [tpp ]  gzstream
> |   |-- [tpp ]  libarchive
> |   `-- [tpp ]  libgd
> |-- [apache  ]  log
> |-- [tpp ]  man
> |   |-- [tpp ]  man1
> |   `-- [tpp ]  man3
> |-- [tpp ]  schema
> `-- [apache  ]  users
> `-- [apache  ]  guest
>
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> 
> .
>

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Re: [spctools-discuss] stuck with problem making tpp

['David Shteynberg' via spctools-discuss]

Also, I wouldn't recommend using make -k because then you get errors with
linking of the sort you are seeing because prerequisite dependencies are
not being built properly so downstream linking of applications to
dependencies fails.

Can you send the actual errors that are generated when you run make all for
the first time on a fresh source tree as those are likely to hold
additional clues?  Also if you are able to provide access to the machine,
or a cloud machine with the same configuration and compilation problem, so
I can log in that would help me troubleshoot the issue.

Thanks!
-David

On Tue, Jun 7, 2022 at 9:02 PM Malcolm Cook  wrote:

> Hi,
>
> I am following &  adapting TPP 6.1.0: Installing on Ubuntu 20.04 LTS
> 
> for our centos 7 environment.
>
> Here are some notes and problems I've encountered so far.
>
> I am building as non privileged user, proceeding as follows:
>
> # create environment for building
> export LD_LIBRARY_PATH=/usr/lib64:${LD_LIBRARY_PATH} ## for
> {libc,libm,libpthreads} else error: "ld: cannot find -lc"
>
> source /opt/rh/devtoolset-9/enable  # enable RED HAT DEVELOPER TOOLSET 9.1
> 
>
> I am compiling with:
>
> make info
> ARCH = x86_64
> VENDOR = redhat
> SYSTEM = linux
> OS = Linux
>
> TPP_VERSION = 6.1.0
> TPP_RELEASE = Parhelion
> TPP_BUILDID = TPP v6.1.0 Parhelion, Build 202206071204-exported
> (Linux-x86_64)
>
> SRC_DIR = /n/sci/SCI-004255-ZFPROT/tpp/svn/trans_proteomic_pipeline
>   BUILD_DIR =
> /n/sci/SCI-004255-ZFPROT/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64-release
> INSTALL_DIR = /usr/local/tpp
>
>TPP_HOME = /usr/local/tpp
> TPP_DATADIR = /data/tpp
> TPP_BASEURL = /tpp
> TPP_DATAURL = /tpp/data
>
>  MZ5_SUPPORT is not enabled
>
> I found as advised that I had to call `make all` many times
>
> The first time created some directories and touch some files and them
> terminated with error:
>
> make: *** No rule to make target
> '/n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/html/',
> needed by 'd3'.  Stop.
>
> The second time halted without an error without compiling anything,
> finally printing:
>
> ### ...done unpacking Boost source
>
> The 3rd through 6th time compile successively more,  though it produced a
> few warnings which were proceeded past, each of the form:
>
> /bin/sh ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -I..-g -O2 -MT rowcol.lo -MD -MP -MF .deps/rowcol.Tpo -c -o rowcol.lo
> rowcol.c
> warning: On gcc, DLLs can not be built with 'static'.
> warning: It is suggested to use 'static' together with
> 'static'.
>
> The 7th time terminated with error:
>
> /bin/sh ./libtool --silent --mode=link gcc -I./lib -I. -g -O2 -Wall
> -Wmissing-prototypes -Wstrict-prototypes -fexceptions
>  -DHAVE_EXPAT_CONFIG_H -no-undefined -version-info 6:2:5 -rpath
> /n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/lib
>  -o libexpat.la lib/xmlparse.lo lib/xmltok.lo lib/xmlrole.lo
> libtool: link: `lib/xmlparse.lo' is not a valid libtool object
>
> I called make an 8th time, this time as `make -k all` to "keep going" past
> errors and build as many targets as possible.  Many more programs were
> compiled successfully, though a few additional errors were picked up:
>
> /bin/sh ../libtool --mode=link gcc -D_REENTRANT -g -O2 -version-info 2:0:0
>  -o libfloatfann.la -rpath
> /n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/lib
>  floatfann.lo
> libtool: link: `floatfann.lo' is not a valid libtool object
>
> I'd be much obliged if anyone with more experience with tpp and gcc could
> comment or make any suggestions on moving forward with how to address any
> of the above errors.
>
> Thanks,
>
> Malcolm
>
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> 
> .
>

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Re: [spctools-discuss] stuck with problem making tpp

['David Shteynberg' via spctools-discuss]

Dear Malcolm,

Sorry you are having trouble building the TPP on centos 7.  There are many
ways you can use the TPP both on the cloud and locally in virtual machines
which would not require you to build the tools from source.  Nevertheless,
the latest release of the TPP has been updated to the c++14 standard yet
older versions of gcc don't support this standard, which might be causing
you problems.  Can you verify that your version of gcc supports c++14?

Thank you,
-David


On Tue, Jun 7, 2022 at 9:02 PM Malcolm Cook  wrote:

> Hi,
>
> I am following &  adapting TPP 6.1.0: Installing on Ubuntu 20.04 LTS
> 
> for our centos 7 environment.
>
> Here are some notes and problems I've encountered so far.
>
> I am building as non privileged user, proceeding as follows:
>
> # create environment for building
> export LD_LIBRARY_PATH=/usr/lib64:${LD_LIBRARY_PATH} ## for
> {libc,libm,libpthreads} else error: "ld: cannot find -lc"
>
> source /opt/rh/devtoolset-9/enable  # enable RED HAT DEVELOPER TOOLSET 9.1
> 
>
> I am compiling with:
>
> make info
> ARCH = x86_64
> VENDOR = redhat
> SYSTEM = linux
> OS = Linux
>
> TPP_VERSION = 6.1.0
> TPP_RELEASE = Parhelion
> TPP_BUILDID = TPP v6.1.0 Parhelion, Build 202206071204-exported
> (Linux-x86_64)
>
> SRC_DIR = /n/sci/SCI-004255-ZFPROT/tpp/svn/trans_proteomic_pipeline
>   BUILD_DIR =
> /n/sci/SCI-004255-ZFPROT/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64-release
> INSTALL_DIR = /usr/local/tpp
>
>TPP_HOME = /usr/local/tpp
> TPP_DATADIR = /data/tpp
> TPP_BASEURL = /tpp
> TPP_DATAURL = /tpp/data
>
>  MZ5_SUPPORT is not enabled
>
> I found as advised that I had to call `make all` many times
>
> The first time created some directories and touch some files and them
> terminated with error:
>
> make: *** No rule to make target
> '/n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/html/',
> needed by 'd3'.  Stop.
>
> The second time halted without an error without compiling anything,
> finally printing:
>
> ### ...done unpacking Boost source
>
> The 3rd through 6th time compile successively more,  though it produced a
> few warnings which were proceeded past, each of the form:
>
> /bin/sh ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -I..-g -O2 -MT rowcol.lo -MD -MP -MF .deps/rowcol.Tpo -c -o rowcol.lo
> rowcol.c
> warning: On gcc, DLLs can not be built with 'static'.
> warning: It is suggested to use 'static' together with
> 'static'.
>
> The 7th time terminated with error:
>
> /bin/sh ./libtool --silent --mode=link gcc -I./lib -I. -g -O2 -Wall
> -Wmissing-prototypes -Wstrict-prototypes -fexceptions
>  -DHAVE_EXPAT_CONFIG_H -no-undefined -version-info 6:2:5 -rpath
> /n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/lib
>  -o libexpat.la lib/xmlparse.lo lib/xmltok.lo lib/xmlrole.lo
> libtool: link: `lib/xmlparse.lo' is not a valid libtool object
>
> I called make an 8th time, this time as `make -k all` to "keep going" past
> errors and build as many targets as possible.  Many more programs were
> compiled successfully, though a few additional errors were picked up:
>
> /bin/sh ../libtool --mode=link gcc -D_REENTRANT -g -O2 -version-info 2:0:0
>  -o libfloatfann.la -rpath
> /n/sci/SCI-004255-ZFPROT/tpp/release_6-1-0/build/linux-x86_64-release/lib
>  floatfann.lo
> libtool: link: `floatfann.lo' is not a valid libtool object
>
> I'd be much obliged if anyone with more experience with tpp and gcc could
> comment or make any suggestions on moving forward with how to address any
> of the above errors.
>
> Thanks,
>
> Malcolm
>
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> 
> .
>

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Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available

['David Shteynberg' via spctools-discuss]

Hi Malcolm,

Thanks for your interest in the TPP.
I think your url has a mistake in it.  Please try the following command:

svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6-1-0


Cheers,
-David

On Tue, Jun 7, 2022 at 3:44 PM Malcolm Cook  wrote:

> Hi,
>
> I am checking out again from the release_6.1.0 since my `make all` is
> problematic, I want to start over, and `make clean` seems perhaps
> incomplete in its cleaning.
>
> Alas I encounter this error whose workaround I can not guess:
>
> svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0
> svn: E17: URL '
> http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0' doesn't exist
>
>
> On Tuesday, June 7, 2022 at 12:37:31 AM UTC-5 Luis wrote:
>
>> Hi Malcolm,
>> Thank you for the congrats, and for catching that in our build notes; we
>> will correct it soon.  In the "Pulling from Sourceforge" section, just
>> follow the commented-out command instead of the last one:
>>
>> #svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0 
>> <- this one; remove the leading pound sign
>> svn checkout 
>> http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline   < 
>> not this one
>>
>>
>> As of tonight, though, the trunk code is still virtually identical to
>> what is tagged as release_6.1.0, so it should work fine.
>>
>> Let us know if you run into any other issues.
>>
>> Thank you for using TPP!
>> --Luis
>>
>>
>> On Mon, Jun 6, 2022 at 10:04 PM malcook  wrote:
>>
>>> Congrats on the new release.
>>>
>>> You will probably want to modify these instructions
>>> which
>>> still advise to download from trunk.
>>>
>>> I just followed  them.
>>>
>>> Should I still expect this to work satisfactorily?
>>>
>>> Thanks
>>>
>>> On Friday, June 3, 2022 at 3:23:19 AM UTC-5 Luis wrote:
>>>
 Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.1.0
 "Parhelion"

 We are proud to offer a major update to the Trans-Proteomic Pipeline
 (TPP) software, release 6.1.0.  The software is available for Windows as
 well as Linux from all the usual locations (please see the section below,
 "Getting the TPP Software").  Most users are recommended to use the Windows
 installer, which installs and configures TPP and other required software,
 such as a web server.  For advanced users who need to customize TPP, or for
 those who run on Linux or OS X, the source code can be downloaded.


 *Release Notes *
 Release notes on the most important new features, changes, and known
 issues are available at:

 http://tools.proteomecenter.org/wiki/index.php?title=TPP:6.1.0_Release_Notes


 *Getting the TPP Software*
 Download the TPP version 6.1.0 native windows installer from the
 Sashimi SourceForge project file release page:
  https://sourceforge.net/projects/sashimi/files/Trans-Proteomic
 Pipeline (TPP)/TPP v6.1 (Parhelion) rev 0/

 Everyone is encouraged to read and contribute to our wiki, at
   http://tools.proteomecenter.org/wiki/

 For guides to installing and using our software, please see our wiki:
   http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

 For downloading the source code, please go to the following link:
   http://sourceforge.net/projects/sashimi/files/  and find the 6.1.0
 source code .zip package
 or, check out the code directly from svn:
   svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_6-1-0

 For building from source, please refer to the README and INSTALL files
 in src/ directory of TPP as well as the wiki.


 *Acknowledgements*
 The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers
 who contributed to this release from ISB.  Thanks to developers and users
 from the TPP's user community who also provided feedback and code
 contributions.


 --
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>>>
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Re: [spctools-discuss] TPP 6.1.0 rc9 Missing module in Perl installation

['David Shteynberg' via spctools-discuss]

Dear Juergen,

Thank you very much for pointing this out.   We will be sure to have this
patched for the official release.

Cheers,
-David

On Fri, Apr 22, 2022 at 6:43 AM Juergen Bartel <
juergen.bar...@uni-greifswald.de> wrote:

> Dear TPP developers,
>
> I tried the release candidate of TPP 6.1 today and observed an error
> during the execution of xinteract:
>
> PeptideProphet runs through the iterations and successfully tests mixture
> model qualities but than fails when it runs ProphetModels.pl
>
> The error message is:
> "Can't locate XML/Parser.pm in @INC (you may need to install the
> XML::Parser module) (@INC contains:...)" for line 36
>
> As I activated the checkbox to install Perl together with the TPP I guess
> this module is missing from the installation?
>
> Best,
> Juergen
>
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> 
> .
>

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Re: [spctools-discuss] Libra on MS3-based TMT quantification

['David Shteynberg' via spctools-discuss]

Great!  Thank you.

On Wed, Apr 6, 2022, 7:04 AM Shagun Gupta  wrote:

> Hi David
>
> Apologies, for some reason my post that it all worked out never made it
> through. Instead one of my older replies I think got posted again. Sorry
> for the confusion and thank you for your help!
>
> Shagun
>
> On Tuesday, April 5, 2022 at 3:09:59 PM UTC-4 David Shteynberg wrote:
>
>> Hello Shagun,
>>
>> Thank you for sharing your complete dataset.  I still found the following
>> in the conditions file you included:
>> TMT10_VB297695_condition.xml
>>
>>   
>>
>>
>> This should be set to 0.001 for this analysis to work on your type of
>> label.  I am attaching the condition file with this change included so you
>> can rerun Libra using the condition file attached.  Please make sure the
>> tolerance is correct in the file when you try running Libra again and if
>> you still see a problem please provide your TPP results interact* files
>> etc...
>>
>> Cheers,
>> -David
>>
>>
>>
>> On Fri, Apr 1, 2022 at 10:03 PM Shagun Gupta  wrote:
>>
>>> The zip folder for the files can be found here:
>>> https://drive.google.com/drive/folders/1hnR2igUXM_K-Pld2xspikeu_xnLGUdMc?usp=sharing
>>>
>>> Let me know if you have any issues.
>>>
>>> Best
>>> Shagun
>>>
>>> On Friday, March 25, 2022 at 1:34:57 PM UTC-4 David Shteynberg wrote:
>>>
>>>> Please place your files on a shared drive and send me a link.
>>>>
>>>> On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta 
>>>> wrote:
>>>>
>>>>> Hi David
>>>>>
>>>>> Could you suggest a good email to reach you with? I can share the
>>>>> pep.xml's and Libra condition file that way?
>>>>>
>>>>> -Shagun
>>>>>
>>>>> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote:
>>>>>
>>>>>> Hello Shagun,
>>>>>>
>>>>>> Thank you for your email and interest in the TPP.  I have recently
>>>>>> been comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that
>>>>>> produced by TPP's Libra.  As far as I can tell, when I run and compare 
>>>>>> the
>>>>>> quantities (intensities) they are mostly the same between Libra (without
>>>>>> isotopic impurity correction and 0 pseudocounts) and the
>>>>>> ProteomeDiscoverer/Byonic.  Execution of Libra is defined in the
>>>>>> conditions.xml file that has to be defined for each Libra run.  I would 
>>>>>> be
>>>>>> happy to take a look at your data and analysis to see if it can be placed
>>>>>> on the right path for the Libra analysis to work.  Please post your 
>>>>>> results
>>>>>> somewhere I can download and test.
>>>>>>
>>>>>> Cheers,
>>>>>> -David
>>>>>>
>>>>>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta 
>>>>>> wrote:
>>>>>>
>>>>>>> Hello
>>>>>>>
>>>>>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
>>>>>>> identification and MS3-based quantification of TMT datasets and we were
>>>>>>> trying to benchmark with an artificial yeast and mammalian spiked 
>>>>>>> dataset
>>>>>>> with known fold-change (FC) values. However we observe drastically
>>>>>>> different values than expected, something we don't observe with other
>>>>>>> search engines for the same dataset.
>>>>>>>
>>>>>>> Has this issue been encountered before/ is there something obviously
>>>>>>> wrong when running with TPP that might cause this? Happy to provide 
>>>>>>> further
>>>>>>> details on the dataset and parameters used to run with (most of them
>>>>>>> default apart from additions like static modification for TMT and
>>>>>>> specification of MS3 for quantification among others).
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Shagun
>>>>>>>
>>>>>>> --
>>>>>>> You received this message because you are subscribed to the Google
>>>>>>> Groups "spctools-dis

Re: [spctools-discuss] Libra on MS3-based TMT quantification

['David Shteynberg' via spctools-discuss]

Hello Shagun,

Thank you for sharing your complete dataset.  I still found the following
in the conditions file you included:
TMT10_VB297695_condition.xml

  


This should be set to 0.001 for this analysis to work on your type of
label.  I am attaching the condition file with this change included so you
can rerun Libra using the condition file attached.  Please make sure the
tolerance is correct in the file when you try running Libra again and if
you still see a problem please provide your TPP results interact* files
etc...

Cheers,
-David



On Fri, Apr 1, 2022 at 10:03 PM Shagun Gupta  wrote:

> The zip folder for the files can be found here:
> https://drive.google.com/drive/folders/1hnR2igUXM_K-Pld2xspikeu_xnLGUdMc?usp=sharing
>
> Let me know if you have any issues.
>
> Best
> Shagun
>
> On Friday, March 25, 2022 at 1:34:57 PM UTC-4 David Shteynberg wrote:
>
>> Please place your files on a shared drive and send me a link.
>>
>> On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta  wrote:
>>
>>> Hi David
>>>
>>> Could you suggest a good email to reach you with? I can share the
>>> pep.xml's and Libra condition file that way?
>>>
>>> -Shagun
>>>
>>> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote:
>>>
>>>> Hello Shagun,
>>>>
>>>> Thank you for your email and interest in the TPP.  I have recently been
>>>> comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced
>>>> by TPP's Libra.  As far as I can tell, when I run and compare the
>>>> quantities (intensities) they are mostly the same between Libra (without
>>>> isotopic impurity correction and 0 pseudocounts) and the
>>>> ProteomeDiscoverer/Byonic.  Execution of Libra is defined in the
>>>> conditions.xml file that has to be defined for each Libra run.  I would be
>>>> happy to take a look at your data and analysis to see if it can be placed
>>>> on the right path for the Libra analysis to work.  Please post your results
>>>> somewhere I can download and test.
>>>>
>>>> Cheers,
>>>> -David
>>>>
>>>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta 
>>>> wrote:
>>>>
>>>>> Hello
>>>>>
>>>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
>>>>> identification and MS3-based quantification of TMT datasets and we were
>>>>> trying to benchmark with an artificial yeast and mammalian spiked dataset
>>>>> with known fold-change (FC) values. However we observe drastically
>>>>> different values than expected, something we don't observe with other
>>>>> search engines for the same dataset.
>>>>>
>>>>> Has this issue been encountered before/ is there something obviously
>>>>> wrong when running with TPP that might cause this? Happy to provide 
>>>>> further
>>>>> details on the dataset and parameters used to run with (most of them
>>>>> default apart from additions like static modification for TMT and
>>>>> specification of MS3 for quantification among others).
>>>>>
>>>>> Thank you,
>>>>> Shagun
>>>>>
>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "spctools-discuss" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to spctools-discu...@googlegroups.com.
>>>>> To view this discussion on the web visit
>>>>> https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com
>>>>> <https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
>>>> --
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Re: [spctools-discuss] Tandem2XML all-15N issue

['David Shteynberg' via spctools-discuss]

Hi Farshad,

Thanks for providing your data and feedback so we can continue to improve
our software.  In this particular case, the mass values used by Tandem2XML
were based on N14  and were likely to result in problematic pepXML
representations of N15 data.  I have added an option to Tandem2XML "N15"
which will use the N15 masses as opposed to N14 masses, when specified by
the user.   I have committed the code change to our repository.  This code
will be available in the next official release of the TPP.

Cheers,
-David

On Wed, Mar 9, 2022 at 11:32 PM Farshad AbdollahNia <
m.f.abdollah...@gmail.com> wrote:

> Hi David,
>
> Thank you for your reply and volunteering to make the changes. Here is a
> link to a stand-alone example data set. Please make sure to change the
> paths in the input file *p08_in.xml* and the taxonomy file
> *prokaryote.xml* to point to your download location.
>
> https://www.dropbox.com/sh/exlp1c2czwqa56c/AACFtEmukZzP9GNEpAXl7SCsa?dl=0
>
> I agree with your proposed changes. Tandem2XML should look for
> user-specified residue masses in its input file (in this example
> *p08_n15.xml*, which is the output from X!Tandem) under the group labeled
> "residue mass parameters" (usually listed at the end of the file) and only
> if this group, or certain residue masses within it, are absent then fall
> back to the default values.
>
> Thanks again for your help and please let me know if I can be of further
> assistance.
>
> Farshad
>
> On Thu, Feb 24, 2022 at 2:32 PM David Shteynberg <
> david.shteynb...@isbscience.org> wrote:
>
>> Dear Farshad,
>>
>> Yes this looks like something that can be corrected.  The fix would use
>> the user-specified mass modification and only when that is not available
>> fall back to the hard-coded value.  I can make the change but would need
>> your data so I can replicate the problem.  Are you able to compress your
>> analysis directory and post it somewhere I can download it?
>>
>> Thanks!
>> -David
>>
>> On Sun, Jan 30, 2022 at 10:28 PM Farshad Abdollah-Nia <
>> m.f.abdollah...@gmail.com> wrote:
>>
>>> Hello everyone,
>>>
>>> I have been getting warnings of the following type from Tandem2XML when
>>> processing all-15N search results:
>>>
>>> WARNING: Unknown modification 'C' (-18.0236) for scan 58137.
>>> WARNING: Unknown modification 'Q' (-18.0236) for scan 66445.
>>>
>>> The all-15N search uses modified residues as well as modified NH3 mass
>>> specification, as detailed here
>>> <https://www.thegpm.org/tandem/api/pmrmf.html>.  However, Tandem2XML
>>> simply uses hard-coded masses for the default special Tandem modifications,
>>> such as pyrolidone <https://www.thegpm.org/tandem/api/pqp.html>, etc:
>>>
>>> // Special X! Tandem n-terminal AA variable modifications
>>>   ModSpecData modSpec;
>>>   modSpec.symbol = '^';
>>>   modSpec.comment = "X! Tandem n-terminal AA variable modification";
>>>
>>>   modSpec.aa = 'E';
>>>   modSpec.mass = -18.0106;
>>>   addModSpec(modSpec, true);
>>>   modSpec.aa = 'Q';
>>>   modSpec.mass = -17.0265;
>>>   addModSpec(modSpec, true);
>>>   if ((long) modsStatic['C'].mass == 57)
>>> {
>>>   modSpec.aa = 'C';
>>>   modSpec.mass = -17.0265;
>>>   addModSpec(modSpec, true);
>>> }
>>>   // deal with quick acetyl
>>>   modSpec.aa = '[';
>>>   modSpec.mass = 42.0106;
>>>   addModSpec(modSpec, true);
>>>
>>> I think these masses should be following the definitions provided by the
>>> user for specific isotopic labeling requirements (2H, 15N, ...) and not
>>> taken as fixed values.
>>>
>>> Does this sound valid to the developers and would a fix be appropriate?
>>>
>>> Thank you,
>>> Farshad
>>>
>>> --
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Re: [spctools-discuss] Libra on MS3-based TMT quantification

['David Shteynberg' via spctools-discuss]

Hello Shagun,

Perhaps I am misunderstand here.  As far as I know, TMT labels are isobaric
and are quantified in the fragment ion spectra.  Any peptide quantified
would have to have the same precursor mass across all TMT labels.
 Presumably there are not that many peptides that are identical between
yeast and human.  The difference in your ratios will only be observable in
the conserved peptides between human and yeast.  Do you have examples of
specific spectra we can consider that work with this approach?  I was able
to run the TPP tools including Libra on this data.

Cheers,
David


On Sat, Mar 26, 2022, 8:11 PM Shagun Gupta  wrote:

> Hi David
>
> So I reran with the changed parameter and the issue still seems to
> persist. I can share the updated results if you'd like as well? Also just
> confirming libra1 - 126, libra2 = 127N and so forth for a TMT10plex for
> example, since the issue is much aggravated in 2 out of three possible
> comparisons. To explain the setup more, yeast proteins are spiked with
> mammalian proteins such that yeast proteins are 10:4:1 (three replicates
> each) with mammalian proteins being (1:1:1) for the same.
>
> Shagun
>
> On Friday, March 25, 2022 at 6:02:55 PM UTC-4 Shagun Gupta wrote:
>
>> Hi David
>>
>> Will do so, thank you! That makes a lot of sense. I have also added the
>> mzXML files but this might be the cause of the discrepancy I see!
>>
>> Thanks
>> Shagun
>>
>> On Friday, March 25, 2022 at 4:42:46 PM UTC-4 David Shteynberg wrote:
>>
>>> Hello Shagun,
>>>
>>> I noticed in your condition file you are using TMT10 with the following
>>> masses:
>>>  
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>
>>>
>>> The difference between neighboring channels is <0.01 at the lowest and
>>> yet you are using tolerance of 0.2:
>>>
>>> 
>>>
>>>
>>> I think the appropriate mass tolerance for this type of labeling should
>>> be ~0.001.
>>>
>>> Does that make sense?  Please try running Libra with the mass tolerance
>>> appropriate for this type of label.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta 
>>> wrote:
>>>
>>>> Hi David
>>>>
>>>> Could you suggest a good email to reach you with? I can share the
>>>> pep.xml's and Libra condition file that way?
>>>>
>>>> -Shagun
>>>>
>>>> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote:
>>>>
>>>>> Hello Shagun,
>>>>>
>>>>> Thank you for your email and interest in the TPP.  I have recently
>>>>> been comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that
>>>>> produced by TPP's Libra.  As far as I can tell, when I run and compare the
>>>>> quantities (intensities) they are mostly the same between Libra (without
>>>>> isotopic impurity correction and 0 pseudocounts) and the
>>>>> ProteomeDiscoverer/Byonic.  Execution of Libra is defined in the
>>>>> conditions.xml file that has to be defined for each Libra run.  I would be
>>>>> happy to take a look at your data and analysis to see if it can be placed
>>>>> on the right path for the Libra analysis to work.  Please post your 
>>>>> results
>>>>> somewhere I can download and test.
>>>>>
>>>>> Cheers,
>>>>> -David
>>>>>
>>>>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta 
>>>>> wrote:
>>>>>
>>>>>> Hello
>>>>>>
>>>>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
>>>>>> identification and MS3-based quantification of TMT datasets and we were
>>>>>> trying to benchmark with an artificial yeast and mammalian spiked dataset
>>>>>> with known fold-change (FC) values. However we observe drastically
>>>>>> different values than expected, something we don't observe with other
>>>>>> search engines for the same dataset.
>>>>>>
>>>>>> Has this issue been encountered before/ is there something obviously
>>>>>> wrong when running with TPP that might cause this? Happy to provide 
>>>>>> further
>>>>>> details on the dataset and paramet

Re: [spctools-discuss] Libra on MS3-based TMT quantification

['David Shteynberg' via spctools-discuss]

Hello Shagun,

I noticed in your condition file you are using TMT10 with the following
masses:
 











The difference between neighboring channels is <0.01 at the lowest and yet
you are using tolerance of 0.2:




I think the appropriate mass tolerance for this type of labeling should be
~0.001.

Does that make sense?  Please try running Libra with the mass tolerance
appropriate for this type of label.

Cheers,
-David

On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta  wrote:

> Hi David
>
> Could you suggest a good email to reach you with? I can share the
> pep.xml's and Libra condition file that way?
>
> -Shagun
>
> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote:
>
>> Hello Shagun,
>>
>> Thank you for your email and interest in the TPP.  I have recently been
>> comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced
>> by TPP's Libra.  As far as I can tell, when I run and compare the
>> quantities (intensities) they are mostly the same between Libra (without
>> isotopic impurity correction and 0 pseudocounts) and the
>> ProteomeDiscoverer/Byonic.  Execution of Libra is defined in the
>> conditions.xml file that has to be defined for each Libra run.  I would be
>> happy to take a look at your data and analysis to see if it can be placed
>> on the right path for the Libra analysis to work.  Please post your results
>> somewhere I can download and test.
>>
>> Cheers,
>> -David
>>
>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta  wrote:
>>
>>> Hello
>>>
>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
>>> identification and MS3-based quantification of TMT datasets and we were
>>> trying to benchmark with an artificial yeast and mammalian spiked dataset
>>> with known fold-change (FC) values. However we observe drastically
>>> different values than expected, something we don't observe with other
>>> search engines for the same dataset.
>>>
>>> Has this issue been encountered before/ is there something obviously
>>> wrong when running with TPP that might cause this? Happy to provide further
>>> details on the dataset and parameters used to run with (most of them
>>> default apart from additions like static modification for TMT and
>>> specification of MS3 for quantification among others).
>>>
>>> Thank you,
>>> Shagun
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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> .
>

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Re: [spctools-discuss] Libra on MS3-based TMT quantification

['David Shteynberg' via spctools-discuss]

Hello Shagun,

Also please include your mzML files, which contain the actual data that
Libra quantifies.

Thanks!
-David

On Fri, Mar 25, 2022 at 10:34 AM David Shteynberg <
david.shteynb...@isbscience.org> wrote:

> Please place your files on a shared drive and send me a link.
>
> On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta  wrote:
>
>> Hi David
>>
>> Could you suggest a good email to reach you with? I can share the
>> pep.xml's and Libra condition file that way?
>>
>> -Shagun
>>
>> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote:
>>
>>> Hello Shagun,
>>>
>>> Thank you for your email and interest in the TPP.  I have recently been
>>> comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced
>>> by TPP's Libra.  As far as I can tell, when I run and compare the
>>> quantities (intensities) they are mostly the same between Libra (without
>>> isotopic impurity correction and 0 pseudocounts) and the
>>> ProteomeDiscoverer/Byonic.  Execution of Libra is defined in the
>>> conditions.xml file that has to be defined for each Libra run.  I would be
>>> happy to take a look at your data and analysis to see if it can be placed
>>> on the right path for the Libra analysis to work.  Please post your results
>>> somewhere I can download and test.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta  wrote:
>>>
>>>> Hello
>>>>
>>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
>>>> identification and MS3-based quantification of TMT datasets and we were
>>>> trying to benchmark with an artificial yeast and mammalian spiked dataset
>>>> with known fold-change (FC) values. However we observe drastically
>>>> different values than expected, something we don't observe with other
>>>> search engines for the same dataset.
>>>>
>>>> Has this issue been encountered before/ is there something obviously
>>>> wrong when running with TPP that might cause this? Happy to provide further
>>>> details on the dataset and parameters used to run with (most of them
>>>> default apart from additions like static modification for TMT and
>>>> specification of MS3 for quantification among others).
>>>>
>>>> Thank you,
>>>> Shagun
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "spctools-discuss" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to spctools-discu...@googlegroups.com.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>> --
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>> "spctools-discuss" group.
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>> email to spctools-discuss+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
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>> <https://groups.google.com/d/msgid/spctools-discuss/7a0b1188-7c5f-4528-9e90-282b860e7627n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>

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Re: [spctools-discuss] Libra on MS3-based TMT quantification

['David Shteynberg' via spctools-discuss]

Please place your files on a shared drive and send me a link.

On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta  wrote:

> Hi David
>
> Could you suggest a good email to reach you with? I can share the
> pep.xml's and Libra condition file that way?
>
> -Shagun
>
> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote:
>
>> Hello Shagun,
>>
>> Thank you for your email and interest in the TPP.  I have recently been
>> comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced
>> by TPP's Libra.  As far as I can tell, when I run and compare the
>> quantities (intensities) they are mostly the same between Libra (without
>> isotopic impurity correction and 0 pseudocounts) and the
>> ProteomeDiscoverer/Byonic.  Execution of Libra is defined in the
>> conditions.xml file that has to be defined for each Libra run.  I would be
>> happy to take a look at your data and analysis to see if it can be placed
>> on the right path for the Libra analysis to work.  Please post your results
>> somewhere I can download and test.
>>
>> Cheers,
>> -David
>>
>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta  wrote:
>>
>>> Hello
>>>
>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
>>> identification and MS3-based quantification of TMT datasets and we were
>>> trying to benchmark with an artificial yeast and mammalian spiked dataset
>>> with known fold-change (FC) values. However we observe drastically
>>> different values than expected, something we don't observe with other
>>> search engines for the same dataset.
>>>
>>> Has this issue been encountered before/ is there something obviously
>>> wrong when running with TPP that might cause this? Happy to provide further
>>> details on the dataset and parameters used to run with (most of them
>>> default apart from additions like static modification for TMT and
>>> specification of MS3 for quantification among others).
>>>
>>> Thank you,
>>> Shagun
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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> .
>

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Re: [spctools-discuss] Libra on MS3-based TMT quantification

['David Shteynberg' via spctools-discuss]

Hello Shagun,

Thank you for your email and interest in the TPP.  I have recently been
comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced
by TPP's Libra.  As far as I can tell, when I run and compare the
quantities (intensities) they are mostly the same between Libra (without
isotopic impurity correction and 0 pseudocounts) and the
ProteomeDiscoverer/Byonic.  Execution of Libra is defined in the
conditions.xml file that has to be defined for each Libra run.  I would be
happy to take a look at your data and analysis to see if it can be placed
on the right path for the Libra analysis to work.  Please post your results
somewhere I can download and test.

Cheers,
-David

On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta  wrote:

> Hello
>
> Our lab has been trying to use Libra to quantify MS2 (Ion-trap)
> identification and MS3-based quantification of TMT datasets and we were
> trying to benchmark with an artificial yeast and mammalian spiked dataset
> with known fold-change (FC) values. However we observe drastically
> different values than expected, something we don't observe with other
> search engines for the same dataset.
>
> Has this issue been encountered before/ is there something obviously wrong
> when running with TPP that might cause this? Happy to provide further
> details on the dataset and parameters used to run with (most of them
> default apart from additions like static modification for TMT and
> specification of MS3 for quantification among others).
>
> Thank you,
> Shagun
>
> --
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> "spctools-discuss" group.
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> https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com
> 
> .
>

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Re: [spctools-discuss] Tandem2XML all-15N issue

['David Shteynberg' via spctools-discuss]

Dear Farshad,

Yes this looks like something that can be corrected.  The fix would use the
user-specified mass modification and only when that is not available fall
back to the hard-coded value.  I can make the change but would need your
data so I can replicate the problem.  Are you able to compress your
analysis directory and post it somewhere I can download it?

Thanks!
-David

On Sun, Jan 30, 2022 at 10:28 PM Farshad Abdollah-Nia <
m.f.abdollah...@gmail.com> wrote:

> Hello everyone,
>
> I have been getting warnings of the following type from Tandem2XML when
> processing all-15N search results:
>
> WARNING: Unknown modification 'C' (-18.0236) for scan 58137.
> WARNING: Unknown modification 'Q' (-18.0236) for scan 66445.
>
> The all-15N search uses modified residues as well as modified NH3 mass
> specification, as detailed here
> .  However, Tandem2XML
> simply uses hard-coded masses for the default special Tandem modifications,
> such as pyrolidone , etc:
>
> // Special X! Tandem n-terminal AA variable modifications
>   ModSpecData modSpec;
>   modSpec.symbol = '^';
>   modSpec.comment = "X! Tandem n-terminal AA variable modification";
>
>   modSpec.aa = 'E';
>   modSpec.mass = -18.0106;
>   addModSpec(modSpec, true);
>   modSpec.aa = 'Q';
>   modSpec.mass = -17.0265;
>   addModSpec(modSpec, true);
>   if ((long) modsStatic['C'].mass == 57)
> {
>   modSpec.aa = 'C';
>   modSpec.mass = -17.0265;
>   addModSpec(modSpec, true);
> }
>   // deal with quick acetyl
>   modSpec.aa = '[';
>   modSpec.mass = 42.0106;
>   addModSpec(modSpec, true);
>
> I think these masses should be following the definitions provided by the
> user for specific isotopic labeling requirements (2H, 15N, ...) and not
> taken as fixed values.
>
> Does this sound valid to the developers and would a fix be appropriate?
>
> Thank you,
> Farshad
>
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> 
> .
>

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Re: [spctools-discuss] Re: TPP Comet search time-out

['David Shteynberg' via spctools-discuss]

Hi Will,

Thanks for posting your question.
This is due to a timeout setting in the webserver.  Thankfully there is a
simple fix:

https://groups.google.com/g/spctools-discuss/c/ZNXMkdB9Y48/m/TYcnPIHgBwAJ

In Windows the steps are :

1. Edit this file:  C:\TPP\conf\httpd-tpp.conf .

2. Change the timeout to a large number of seconds:

 Timeout 864000

(this will set the timeout to 10 days!)

3. Restart the Apache webserver (you can also find it in Services)

Cheers,
-David

On Thu, Dec 16, 2021 at 8:20 AM Will Comstock  wrote:

> I have also been encountering this issue and would love to hear a
> solution. The search still reads as "Running" but simply stops searching
> any more mzML files. Depending on the size of my  files, the search times
> out at different points, but will almost never search more than 8 files at
> a time.
>
> Happy to provide an example dataset + parameters + FASTA file if anyone
> wants to try and replicate the timeout.
>
> -Will
>
> On Wednesday, November 10, 2021 at 1:32:09 AM UTC-5 steven...@gmail.com
> wrote:
>
>> Hi everyone,
>>
>> I've been using TPP for a little while now for the analysis of my data. I
>> have been using Comet to perform database searching on a large number of
>> mzml files and have noticed that the analysis will usually time out after
>> about 6 hours. In this case, I will remove the mzml files that have been
>> successfully processed and then re-run comet. Is this job time-out an
>> inherent part of TPP, or is it a setting that can be changed? If the
>> latter, are there any risks in running the analysis for over 6 hours?
>>
>> Thanks in advance for any advice
>> Steven
>>
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> 
> .
>

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Re: [spctools-discuss] PTMProphet flags

['David Shteynberg' via spctools-discuss]

Dear Pedro,

Sorry about the delay in my response to your query.


I am not sure what version of PTMProphet you are using, we are currently on
TPP 6.0.0 official release (6.1.0 available as a release candidate.)

Here is some more information about the options you are interested in:



*LABILITY Compute Lability of PTMs*

  Compute the "lability" of the PTM, the likelihood that some number PTMs
of a given type in the PSM have fallen off the peptide backbone, given the
fragment spectrum information.


*DIRECT   Use only direct evidence for evaluating PTM site probabilities*

   This option forces PTMProphet to use only fragments that retain the PTM
and thus constitute "direct" evidence of PTM for site localization

*AUTODIRECT   Use direct evidence when the lability is high, use in
combination with LABILITY*

  This option is used in combination with the LABILITY option, which
estimates how "labile" (likely to fall off) is the PTM in the given PSM.
When  the estimated lability is high and AUTODIRECT enabled, PTMProphet
will use only direct evidence peaks for PTM site localization.


*IFRAGS   Use internal fragments for localization (default: do not use
internal fragments)*

  This option enables the use of internal fragments for PTM site
localization.


*EXCLUDEMASSDIFFMIN=  Minimum mass difference excluded for
 MASSDIFFFMODE analysis (default=0).*

*EXCLUDEMASSDIFFMAX=  Maximum mass difference excluded for
MASSDIFFFMODE analysis (default=0).*



*MASSDIFFMODE Treat the mass difference between measured and
theoretical mass as a modification and localize*

  This option enables treatment of the observed mass difference like any
other PTM and localizing the mass difference on the peptide backbone, this
option is used with EXCLUDEMASSDIFFMIN= and EXCLUDEMASSDIFFMAX= to limit
localization of mass differences as defined by the user.

Please write back if you have additional questions or problems with the
TPP.  The usage statement for PTMProphetParser (part of the TPP
www.tppms.org) is available when you run PTMProphetParser on the
commandline without any inputs.

Cheers,
-David



On Mon, Oct 18, 2021 at 8:12 AM Pedro Cardoso 
wrote:

> Hi,
>
> I am using PTMProphet (v4.0.0) but I can't really understand what some of
> the optional flags are supposed to do.
> I have went through the publication and its supplementary figures but
> still can't know for sure what changes when some of the flags are used.
> The flags that seem interesting to me are:
> --direct
> --autodirect
> --ifrags
> --lability
> --massdiffmode - this should be used with open database searches, correct??
>
>
> Can you please provide more detailed information of these flags? Or maybe
> point me to some other documentation other than the published article and
> the basic description of each flag?
>
> Thank you,
> Pedro
>
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> 
> .
>

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Re: [spctools-discuss] Precursor Intensity after Comet search

['David Shteynberg' via spctools-discuss]

Hi Will,

You can use option -PREC in advanced options for xinteract "Analyze
Peptides" results to populate this column.Alternatively you can run
InteractParser with -I flag to get the same values in the pepXML results.

Cheers,
-David

On Thu, Sep 16, 2021 at 8:11 AM Will Comstock  wrote:

> Hello,
>
> After Comet searching mzXML files, appending the "Precursor Intensity"
> column in the pepXML viewer reveals that it contains no values. Is there a
> way to make Comet retrieve/retain precursor intensities for later use?
> Would running XPRESS in label-free mode essentially accomplish this? I am
> using TPP 6.0 for these analyses.
>
> Respectfully,
> -Will Comstock
>
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> 
> .
>

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Re: [spctools-discuss] TPP 6.0 Libra Error

['David Shteynberg' via spctools-discuss]

Great thanks for finding the bug Will!  The code will be part of the next
release.

On Sat, Sep 4, 2021 at 2:57 PM Will Comstock  wrote:

> Hi David,
>
> It works! Thanks very much for addressing this issue so promptly.
>
> Best,
> -Will
>
> On Friday, September 3, 2021 at 9:24:36 PM UTC-4 David Shteynberg wrote:
>
>> Hi Will,
>>
>> I was able to trace this to a memory issue in the code and correct it.
>>  I have posted a patched version here:
>>
>>
>> https://drive.google.com/file/d/1jiGuyLDC1E504GvnG_MqX7R6J4NWe_2D/view?usp=sharing
>>
>>
>> Replace your copy in C:\TPP\bin or where you installed your TPP.
>>
>>
>> Please let me know if you have any questions or issues with the new
>> executable.
>>
>> Thanks,
>> -David
>>
>> On Fri, Sep 3, 2021 at 9:34 AM Will Comstock  wrote:
>>
>>> Hi David,
>>>
>>> Here is a Google Drive folder containing all the files used in the
>>> search. A .txt file with the error message I encountered is included, as
>>> well as a screenshot of the Peptide Prophet parameters I used.
>>>
>>>
>>> https://drive.google.com/drive/folders/1xS8GdvOFw7tVMNLzObC_3tz1cttX_kLw?usp=sharing
>>>
>>> I appreciate the help!
>>> -Will
>>>
>>> On Friday, September 3, 2021 at 12:21:13 PM UTC-4 David Shteynberg wrote:
>>>
>>>> Hello William,
>>>>
>>>> Sorry to hear you are having trouble with Libra.  If you are able to
>>>> post the data for me to reproduce the problem I will attempt to patch it 
>>>> up.
>>>>
>>>> Thank you!
>>>>
>>>> -David
>>>>
>>>>
>>>>
>>>> On Fri, Sep 3, 2021 at 8:02 AM Will Comstock  wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Our lab just updated from 5.2 to 6.0 and is testing some datasets that
>>>>> were formerly searched with 5.2.
>>>>>
>>>>> We are now consistently encountering an error when running Libra after
>>>>> PeptideProphet, preventing the reporter ion quantitation from completing.
>>>>> The resulting interact.pep.xml is still able to be opened, there is just 
>>>>> no
>>>>> Libra result appended to the table.
>>>>>
>>>>> Here is the Libra error encountered:
>>>>> [image: TPP6_LibraError.PNG]
>>>>>
>>>>> The return code is 29696. What could be causing this, and how might we
>>>>> try fixing it?
>>>>>
>>>>> Thank you,
>>>>> -Will Comstock
>>>>>
>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "spctools-discuss" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to spctools-discu...@googlegroups.com.
>>>>> To view this discussion on the web visit
>>>>> https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com
>>>>> <https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
>>>> --
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>>> https://groups.google.com/d/msgid/spctools-discuss/107618af-5a58-4508-84eb-23a6598121a9n%40googlegroups.com
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>>> .
>>>
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Re: [spctools-discuss] TPP 6.0 Libra Error

['David Shteynberg' via spctools-discuss]

Hi Will,

I was able to trace this to a memory issue in the code and correct it.   I
have posted a patched version here:

https://drive.google.com/file/d/1jiGuyLDC1E504GvnG_MqX7R6J4NWe_2D/view?usp=sharing


Replace your copy in C:\TPP\bin or where you installed your TPP.


Please let me know if you have any questions or issues with the new
executable.

Thanks,
-David

On Fri, Sep 3, 2021 at 9:34 AM Will Comstock  wrote:

> Hi David,
>
> Here is a Google Drive folder containing all the files used in the search.
> A .txt file with the error message I encountered is included, as well as a
> screenshot of the Peptide Prophet parameters I used.
>
>
> https://drive.google.com/drive/folders/1xS8GdvOFw7tVMNLzObC_3tz1cttX_kLw?usp=sharing
>
> I appreciate the help!
> -Will
>
> On Friday, September 3, 2021 at 12:21:13 PM UTC-4 David Shteynberg wrote:
>
>> Hello William,
>>
>> Sorry to hear you are having trouble with Libra.  If you are able to post
>> the data for me to reproduce the problem I will attempt to patch it up.
>>
>> Thank you!
>>
>> -David
>>
>>
>>
>> On Fri, Sep 3, 2021 at 8:02 AM Will Comstock  wrote:
>>
>>> Hello,
>>>
>>> Our lab just updated from 5.2 to 6.0 and is testing some datasets that
>>> were formerly searched with 5.2.
>>>
>>> We are now consistently encountering an error when running Libra after
>>> PeptideProphet, preventing the reporter ion quantitation from completing.
>>> The resulting interact.pep.xml is still able to be opened, there is just no
>>> Libra result appended to the table.
>>>
>>> Here is the Libra error encountered:
>>> [image: TPP6_LibraError.PNG]
>>>
>>> The return code is 29696. What could be causing this, and how might we
>>> try fixing it?
>>>
>>> Thank you,
>>> -Will Comstock
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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> .
>

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Re: [spctools-discuss] TPP 6.0 Libra Error

['David Shteynberg' via spctools-discuss]

Hi Will,

Thanks for sharing the dataset.  I was able to reproduce the problem.  When
I have a potential solution I will let you know.  Thank you for helping by
reporting the error, it helps us improve the quality of the TPP over time.

-David

On Fri, Sep 3, 2021 at 9:34 AM Will Comstock  wrote:

> Hi David,
>
> Here is a Google Drive folder containing all the files used in the search.
> A .txt file with the error message I encountered is included, as well as a
> screenshot of the Peptide Prophet parameters I used.
>
>
> https://drive.google.com/drive/folders/1xS8GdvOFw7tVMNLzObC_3tz1cttX_kLw?usp=sharing
>
> I appreciate the help!
> -Will
>
> On Friday, September 3, 2021 at 12:21:13 PM UTC-4 David Shteynberg wrote:
>
>> Hello William,
>>
>> Sorry to hear you are having trouble with Libra.  If you are able to post
>> the data for me to reproduce the problem I will attempt to patch it up.
>>
>> Thank you!
>>
>> -David
>>
>>
>>
>> On Fri, Sep 3, 2021 at 8:02 AM Will Comstock  wrote:
>>
>>> Hello,
>>>
>>> Our lab just updated from 5.2 to 6.0 and is testing some datasets that
>>> were formerly searched with 5.2.
>>>
>>> We are now consistently encountering an error when running Libra after
>>> PeptideProphet, preventing the reporter ion quantitation from completing.
>>> The resulting interact.pep.xml is still able to be opened, there is just no
>>> Libra result appended to the table.
>>>
>>> Here is the Libra error encountered:
>>> [image: TPP6_LibraError.PNG]
>>>
>>> The return code is 29696. What could be causing this, and how might we
>>> try fixing it?
>>>
>>> Thank you,
>>> -Will Comstock
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/6ced026c-485f-4b4e-8ef1-02fe487234a0n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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> .
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Re: [spctools-discuss] TPP 6.0 Libra Error

['David Shteynberg' via spctools-discuss]

Hello William,

Sorry to hear you are having trouble with Libra.  If you are able to post
the data for me to reproduce the problem I will attempt to patch it up.

Thank you!

-David



On Fri, Sep 3, 2021 at 8:02 AM Will Comstock  wrote:

> Hello,
>
> Our lab just updated from 5.2 to 6.0 and is testing some datasets that
> were formerly searched with 5.2.
>
> We are now consistently encountering an error when running Libra after
> PeptideProphet, preventing the reporter ion quantitation from completing.
> The resulting interact.pep.xml is still able to be opened, there is just no
> Libra result appended to the table.
>
> Here is the Libra error encountered:
> [image: TPP6_LibraError.PNG]
>
> The return code is 29696. What could be causing this, and how might we try
> fixing it?
>
> Thank you,
> -Will Comstock
>
> --
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> 
> .
>

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Re: [spctools-discuss] PTMProphet and best localization score

['David Shteynberg' via spctools-discuss]

Hi Niko,

Thanks for your question and interest in the TPP.

The PepXMLViewer.cgi tool can be used to display, filter and export pepXML
data, including PTMProphet processed results.  PTMProphet computes several
statistics for each PSM and for each PTM analyzed:

Mean Best Probability -- is the average PTMProphet probability of the top
*m* modified sites of a given type in the peptide

Normalized Information Gain -- is the information gain based on the
PTMProphet probabiliy of the top *m* modified sites of a given type in the
peptide

Localized Modification Count -- is the expected number of correct
modifications of a given type localized with certainty on this peptide

For more information about there metrics please refer to the PTMProphet
publication.

The reason you might want to use the more conservative Info Gain metric to
threshold your results is that site probabilities are not directly
comparable between PSMs with different site and PTM counts, but Info Gains
are directly comparable.  E.g. a Mean Best PTM probability of 0.75 on a
peptide with 4 sites and 3 PTMs of the a given type means there is zero
information about the location of those 3 PTMs and it means a different
thing from a  Mean Best PTM probability of 0.75 on a peptide with 4 sites
and 1 PTM where the information regarding the location of the PTM is
greater than zero!

You can set thresholds for any of these metrics on the Filter page in
PepXMLViewer.cgi. Make sure to set it for the correct PTM type.

I hope I have understood your question correctly, please let me know if you
have any more.

Cheers!

-David

On Wed, Aug 18, 2021 at 12:27 AM Niko Pinter 
wrote:

>
> Hi,
>
> thanks for all the effort you put into TPP and PTMProphet.
>
> We are currently analyzing some datasets of synthetic phosphopeptides with
> PTMProphet and wondered where to set the cut-off for the best localization
> score. A score above 0.750 was often used in literature and we tend to use
> a similar cut-off.
>
> Best regards
> Niko Pinter
>
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> .
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Re: [spctools-discuss] xinteract (TPP v5.2.0) not detecting any spectra from comet output

['David Shteynberg' via spctools-discuss]

Hi Damian,

Unfortunately, TPP 5.2.0 is not forward compatible to comet 2020.  We are
working on the 6.0.0 release and have a couple of release candidates
available.   I will post another rc tomorrow.

Cheers,
David

On Sat, Apr 24, 2021, 9:09 AM dfermin  wrote:

> Hello
>
> I performed a search on 4 mzML files against a human proteome file with
> decoys appended. The decoy prefix I'm using is 'rev_'
>
> I ran comet version 2020.01 rev 3 on the mzML file and got out the
> comet-generated pep.xml files.
>
> When I run xinteract on these files  PeptideProphet seems unable to find
> any spectra.
> I've looked at the pep.xml files comet generated and it has all the usual
> features. The files contain the top 5 hits for each spectra.
>
> Any suggestions what might be wrong?
> Thanks in advance for any and all help.
>
> I'm running TPP v5.2.0 on a Centos 7  box in case it helps
> Here is the stdout on the terminal:
> #==
> [dfermin tmp]$ xinteract -Opwd -drev *.pep.xml
>
> xinteract (TPP v5.2.0 Flammagenitus, Build 201904020842-exported
> (Linux-x86_64))
>
> running: "/usr/local/apps/tpp/bin/InteractParser 'interact.pep.xml'
> '01347_H01_P013678_S00_N08_R2.pep.xml'
> '01347_H02_P013678_S00_N16_R2.pep.xml'
> '01347_H03_P013678_S00_N24_R2.pep.xml'
> '01347_H04_P013678_S00_N32_R2.pep.xml' -L'7'"
>  file 1: 01347_H01_P013678_S00_N08_R2.pep.xml
>  file 2: 01347_H02_P013678_S00_N16_R2.pep.xml
>  file 3: 01347_H03_P013678_S00_N24_R2.pep.xml
>  file 4: 01347_H04_P013678_S00_N32_R2.pep.xml
>  processed altogether 203112 results
> INFO: Results written to file: /nfs/md0/testRun2021/interact.pep.xml
> command completed in 104 sec
>
> running: "/usr/local/apps/tpp/bin/DatabaseParser 'interact.pep.xml'"
> command completed in 1 sec
>
> running: "/usr/local/apps/tpp/bin/RefreshParser 'interact.pep.xml'
> '/nfs/md0/tpp.data/human_uniprot_withIsoforms.2021-04-14.plusREV.fa'"
>   - Building Commentz-Walter keyword tree...
>   - Searching the tree...
>   - Linking duplicate entries...
>   - Printing results...
>
> command completed in 62 sec
>
> running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml'
> INSTRWARN DECOYPROBS DECOY=rev"
> Using no error on different instrument types.
> Using Decoy Label "rev".
> Decoy Probabilities will be reported.
>  (Comet)
> init with Comet trypsin
> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>
> INFO: Processing standard MixtureModel ...
>  PeptideProphet  (TPP v5.2.0 Flammagenitus, Build 201904020842-exported
> (Linux-x86_64)) AKeller@ISB
>  read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
>  read in no data
>
> command "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml'
> INSTRWARN DECOYPROBS DECOY=rev" exited with non-zero exit code: 256
> QUIT - the job is incomplete
>
>
>
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Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)

['David Shteynberg' via spctools-discuss]

Will,

Thanks for the update!

Cheers,
David

On Thu, Apr 15, 2021, 6:22 AM Will Comstock  wrote:

> Hi David,
>
> An update just in case anyone else has run into our issue: I copied the
> PTMProphetParser.exe from a 6.0.0 installation over into our current 5.2.0
> installation, and everything is working great thus far!
>
> Thank you for the tip, I appreciate the assistance.
>
> Respectfully,
> -Will
>
> On Tuesday, March 16, 2021 at 8:46:35 PM UTC-4 David Shteynberg wrote:
>
>> Hi Will,
>>
>> There is a release candidate for version 6.0.0 available on sourceforge:
>>
>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v6.0%20%28Release%20Candidates%29/
>>
>> If you do end up trying it let me know if you find any issues.
>>
>> Thanks!
>> -David
>>
>> On Tue, Mar 16, 2021 at 5:14 PM Will Comstock  wrote:
>>
>>> Hi David,
>>>
>>> I'll attempt to re-run PTMProphet analysis on a few problematic datasets
>>> with MAXTHREADS=1.
>>>
>>> I am currently using the version of PTMProphet that came with the
>>> installation of TPP 5.2. Is there a newer version available that I could be
>>> using instead?
>>>
>>> Thanks for your help!
>>> -Will
>>>
>>> On Tuesday, March 16, 2021 at 7:37:58 PM UTC-4 David Shteynberg wrote:
>>>
>>>> Hello Will,
>>>>
>>>> We routinely run PTMProphet on datasets containing multiple hundreds of
>>>> thousands of PSMs. This looks like multithreading issue
>>>> related MAXTHREADS=0 parameter, this should not happen if you use
>>>> MAXTHREADS=1.  I have corrected several bugs related to multithreading in
>>>> the codebase. Which version of PTMProphet are you using?
>>>>
>>>> Thanks,
>>>> -David
>>>>
>>>> On Tue, Mar 16, 2021 at 3:59 PM Will Comstock 
>>>> wrote:
>>>>
>>>>> Hey everyone,
>>>>>
>>>>> I've run into an issue with PTMProphet where occasionally the command
>>>>> will fail for unknown reasons and the resulting ptm.pep.xml cannot be
>>>>> opened with the PepXML viewer. The command log seems to cut off abruptly,
>>>>> as pictured in the attached screenshot. Also attached is the page that
>>>>> appears upon trying to open the ptm.pep.xml.
>>>>>
>>>>> The interact.pep.xml files we're analyzing clock in at about 200 to
>>>>> 250 megabytes. As a workaround, we currently just split the initial batch
>>>>> of pep.xmls into smaller groups before running PeptideProphet and
>>>>> PTMProphet on them again. Sometimes we end up with batches of pep.xmls as
>>>>> small as 3 or 4 files, which is somewhat inconvenient for projects with
>>>>> hundreds of RAW files.
>>>>>
>>>>> Is there another way around this issue? We've tried running it through
>>>>> the command line as well and this problem still crops up frequently.
>>>>> [image: PTMproph_CommandFailed.png]
>>>>> [image: PTMproph_CommandFailed_xmlError.png]
>>>>> Thanks!
>>>>>
>>>>> --
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>>>>> an email to spctools-discu...@googlegroups.com.
>>>>> To view this discussion on the web visit
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>>>>> .
>>>>>
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>>> .
>>>
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> <https://groups.google.com/d/msgid/spctools-discuss/b5eceb74-1e34-4c71-9f09-27b1e266ec89n%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>

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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

['David Shteynberg' via spctools-discuss]

Hi Oded,

I think the old 5.2.0 might be under estimating the error rate as compared
to the new release candidate.   You cannot see the decoys here because of
the settings you used.  However your database has two independent sets of
decoys available DECOY0 and DECOY1.  Can you use one of the set for
PeptideProphet and use the other set to get a decoy count at a given
PeptideProphet probability cutoff.  I suspect the 5.2.0 TPP will show more
unknown decoys than the new release candidate.   Can you test if this is
the case here?  I can run a more in depth analysis when I am back from
vacation next week.

Cheers,
David

On Tue, Apr 13, 2021, 2:07 PM Oded  wrote:

> Dear David,
> This is PeptideProphet issue (we don't use iProphet for this analysis).
> With the search parameters that I sent you followed by running the
> PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM
> -OANEp -dDECOY Seq69478_QE2.pep.xml,*
> and lastly using a cutoff of 1% error rate we obtain with TPP 5.2 2836
> correct assignments and with TPP 6.0 only 2228 correct assignments. The
> probability for 1% error rate is 0.84 in TPP 5.2 and 0.9090 in TPP 6.0).
> In the following link, you will find the interact files (new and old):
> https://www.dropbox.com/t/mwtpCLeEJRLCwbi1
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fl%2FAACfc2b_KukHZAS1VuNo4sPM3gEXyXtDlPE&data=04%7C01%7Coklab%40technion.ac.il%7C342d2db781c2443416b108d8febfbc70%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637539447557029368%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=LBdAB3QsH9rUxvNKMwKjOKYDbQXFxma9dREKgS5siWQ%3D&reserved=0>
> Thanks,
> Oded
>
>
>
> On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote:
>
>> Dear Oded,
>>
>> Thanks for this.  I ran a quick test and I actually observed a few more
>> PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability
>> cutoff for this dataset.  Is the issue you see with PeptideProphet or
>> iProphet results?   Which spectra were getting excluded in the your testing
>> of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain
>> you are using identical analysis parameters for PeptideProphet and what are
>> those parameters?
>>
>> Cheers,
>>
>> David
>>
>> On Mon, Apr 12, 2021, 2:15 PM Oded  wrote:
>>
>>> And also the search results with the new vs the old version (although I
>>> think they are more or less the same):
>>> https://www.dropbox.com/t/8VyBVdeuoWdk982q
>>>
>>>
>>> On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:
>>>
>>>> Hi David,
>>>> You can find the mzML, Comet parameters and FASTA file here:
>>>> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
>>>> The link is valid for 7 days.
>>>> Many thanks,
>>>> Oded
>>>>
>>>> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
>>>>
>>>>> I don't mind taking a crack at it over vacation.   Please let me know
>>>>> where I can pull the data from. I might not have quick solution for you 
>>>>> but
>>>>> I can get started looking for the problem.  Which search engine did you 
>>>>> use
>>>>> here?   I would need mzML data search results and the fasta database to 
>>>>> get
>>>>> started.
>>>>>
>>>>> Thanks!
>>>>>
>>>>>
>>>>>
>>>>> Thanks!
>>>>>
>>>>> On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:
>>>>>
>>>>>> Hi David,
>>>>>> Thank you for the quick reply. We are using TPP v6.0.0-rc14
>>>>>> Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64).
>>>>>> As for the data let me know when you are back and I will transfer you
>>>>>> either the raw file or the search results.
>>>>>> Enjoy your vacation.
>>>>>> Thanks,
>>>>>> Oded
>>>>>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>>>>>>
>>>>>>> Hi Oded,  Which release candidate are you referring to?  The earlier
>>>>>>> candidates may have a bug that is corrected in a later version. If you 
>>>>>>> can
>>>>>>> share some data and specifics about the missing PSMs I can run it here 
>>>>>>> and
>>>>>>> troubleshoot the problem.
>>>>&

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

['David Shteynberg' via spctools-discuss]

Dear Oded,

Thanks for this.  I ran a quick test and I actually observed a few more
PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability
cutoff for this dataset.  Is the issue you see with PeptideProphet or
iProphet results?   Which spectra were getting excluded in the your testing
of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain
you are using identical analysis parameters for PeptideProphet and what are
those parameters?

Cheers,

David

On Mon, Apr 12, 2021, 2:15 PM Oded  wrote:

> And also the search results with the new vs the old version (although I
> think they are more or less the same):
> https://www.dropbox.com/t/8VyBVdeuoWdk982q
>
>
> On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:
>
>> Hi David,
>> You can find the mzML, Comet parameters and FASTA file here:
>> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
>> The link is valid for 7 days.
>> Many thanks,
>> Oded
>>
>> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
>>
>>> I don't mind taking a crack at it over vacation.   Please let me know
>>> where I can pull the data from. I might not have quick solution for you but
>>> I can get started looking for the problem.  Which search engine did you use
>>> here?   I would need mzML data search results and the fasta database to get
>>> started.
>>>
>>> Thanks!
>>>
>>>
>>>
>>> Thanks!
>>>
>>> On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:
>>>
>>>> Hi David,
>>>> Thank you for the quick reply. We are using TPP v6.0.0-rc14
>>>> Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64).
>>>> As for the data let me know when you are back and I will transfer you
>>>> either the raw file or the search results.
>>>> Enjoy your vacation.
>>>> Thanks,
>>>> Oded
>>>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>>>>
>>>>> Hi Oded,  Which release candidate are you referring to?  The earlier
>>>>> candidates may have a bug that is corrected in a later version. If you can
>>>>> share some data and specifics about the missing PSMs I can run it here and
>>>>> troubleshoot the problem.
>>>>>
>>>>> Thanks!
>>>>>
>>>>> David
>>>>>
>>>>> P.S. I am on vacation this week so will troubleshoot next week.
>>>>>
>>>>> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>>>>>
>>>>>> Hi there,
>>>>>> We recently download the TPP 6.0 RC and while using it we noticed
>>>>>> that we obtain fewer peptides IDs than what we got for the same dataset 
>>>>>> and
>>>>>> search output with version 5.2.
>>>>>> Many of the missing peptides seem to have decent Expect value and
>>>>>> MS/MS following a visual inspection.
>>>>>> This seems that this is due to changes in PeptideProphet and are not
>>>>>> related to the search itself that was done with Comet.
>>>>>> Is there any additional parameter that should be included in the new
>>>>>> version in order to restore the missing peptides?
>>>>>> Many thanks,
>>>>>> Oded
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "spctools-discuss" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to spctools-discu...@googlegroups.com.
>>>>>> To view this discussion on the web visit
>>>>>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
>>>>>> <https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>> --
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>>>> Groups "spctools-discuss" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to spctools-discu...@googlegroups.com.
>>>>
>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

['David Shteynberg' via spctools-discuss]

I don't mind taking a crack at it over vacation.   Please let me know where
I can pull the data from. I might not have quick solution for you but I can
get started looking for the problem.  Which search engine did you use
here?   I would need mzML data search results and the fasta database to get
started.

Thanks!



Thanks!

On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:

> Hi David,
> Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent,
> Build 202103031119-8400 (Windows_NT-x86_64).
> As for the data let me know when you are back and I will transfer you
> either the raw file or the search results.
> Enjoy your vacation.
> Thanks,
> Oded
> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>
>> Hi Oded,  Which release candidate are you referring to?  The earlier
>> candidates may have a bug that is corrected in a later version. If you can
>> share some data and specifics about the missing PSMs I can run it here and
>> troubleshoot the problem.
>>
>> Thanks!
>>
>> David
>>
>> P.S. I am on vacation this week so will troubleshoot next week.
>>
>> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>>
>>> Hi there,
>>> We recently download the TPP 6.0 RC and while using it we noticed that
>>> we obtain fewer peptides IDs than what we got for the same dataset and
>>> search output with version 5.2.
>>> Many of the missing peptides seem to have decent Expect value and MS/MS
>>> following a visual inspection.
>>> This seems that this is due to changes in PeptideProphet and are not
>>> related to the search itself that was done with Comet.
>>> Is there any additional parameter that should be included in the new
>>> version in order to restore the missing peptides?
>>> Many thanks,
>>> Oded
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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> .
>

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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

['David Shteynberg' via spctools-discuss]

Hi Oded,  Which release candidate are you referring to?  The earlier
candidates may have a bug that is corrected in a later version. If you can
share some data and specifics about the missing PSMs I can run it here and
troubleshoot the problem.

Thanks!

David

P.S. I am on vacation this week so will troubleshoot next week.

On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:

> Hi there,
> We recently download the TPP 6.0 RC and while using it we noticed that we
> obtain fewer peptides IDs than what we got for the same dataset and search
> output with version 5.2.
> Many of the missing peptides seem to have decent Expect value and MS/MS
> following a visual inspection.
> This seems that this is due to changes in PeptideProphet and are not
> related to the search itself that was done with Comet.
> Is there any additional parameter that should be included in the new
> version in order to restore the missing peptides?
> Many thanks,
> Oded
>
> --
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> "spctools-discuss" group.
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> email to spctools-discuss+unsubscr...@googlegroups.com.
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> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
> 
> .
>

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Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)

['David Shteynberg' via spctools-discuss]

Hi Will,

There is a release candidate for version 6.0.0 available on sourceforge:
https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v6.0%20%28Release%20Candidates%29/

If you do end up trying it let me know if you find any issues.

Thanks!
-David

On Tue, Mar 16, 2021 at 5:14 PM Will Comstock  wrote:

> Hi David,
>
> I'll attempt to re-run PTMProphet analysis on a few problematic datasets
> with MAXTHREADS=1.
>
> I am currently using the version of PTMProphet that came with the
> installation of TPP 5.2. Is there a newer version available that I could be
> using instead?
>
> Thanks for your help!
> -Will
>
> On Tuesday, March 16, 2021 at 7:37:58 PM UTC-4 David Shteynberg wrote:
>
>> Hello Will,
>>
>> We routinely run PTMProphet on datasets containing multiple hundreds of
>> thousands of PSMs. This looks like multithreading issue
>> related MAXTHREADS=0 parameter, this should not happen if you use
>> MAXTHREADS=1.  I have corrected several bugs related to multithreading in
>> the codebase. Which version of PTMProphet are you using?
>>
>> Thanks,
>> -David
>>
>> On Tue, Mar 16, 2021 at 3:59 PM Will Comstock  wrote:
>>
>>> Hey everyone,
>>>
>>> I've run into an issue with PTMProphet where occasionally the command
>>> will fail for unknown reasons and the resulting ptm.pep.xml cannot be
>>> opened with the PepXML viewer. The command log seems to cut off abruptly,
>>> as pictured in the attached screenshot. Also attached is the page that
>>> appears upon trying to open the ptm.pep.xml.
>>>
>>> The interact.pep.xml files we're analyzing clock in at about 200 to 250
>>> megabytes. As a workaround, we currently just split the initial batch of
>>> pep.xmls into smaller groups before running PeptideProphet and PTMProphet
>>> on them again. Sometimes we end up with batches of pep.xmls as small as 3
>>> or 4 files, which is somewhat inconvenient for projects with hundreds of
>>> RAW files.
>>>
>>> Is there another way around this issue? We've tried running it through
>>> the command line as well and this problem still crops up frequently.
>>> [image: PTMproph_CommandFailed.png]
>>> [image: PTMproph_CommandFailed_xmlError.png]
>>> Thanks!
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
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>>> an email to spctools-discu...@googlegroups.com.
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>>> .
>>>
>> --
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Re: [spctools-discuss] job end with error when following PTMprophet tutorial

['David Shteynberg' via spctools-discuss]

Hi Panyue,

Thanks for confirming that it works.  I think after you run that code from
the commandline allowing perl interpreter to process it, at least on my
system it registered the file and allowed me to run it through Petunia the
next time I tried it.  Maybe updatePaths.pl will work for you from Petunia
going forward?  If not it should work the next time you install a TPP
update.

Cheers,
-David

On Wed, Mar 10, 2021 at 10:28 AM Panyue Chen 
wrote:

> Hi David,
>
> Thank you so much! It works for me.
> Just in case other people are in the same situation. I want to
> provide more detail here. I ran the Petunia command line (as in the image)
> in the command prompt of Windows system:
> cd d:/TPP/data/tutorials/Ferries2017/com_tan_HCDOT && d: && D:/TPP/bin/
> updatepaths.pl -v
> d:/TPP/data/tutorials/Ferries2017/com_tan_HCDOT/interact.ipro.pep.xml
>
> [image: command.png]
>
> Best,
> Panyue
>
> On Wed, Mar 10, 2021 at 12:54 AM 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello again,
>>
>> I downloaded the code from sourceforge and replaced my version to test
>> and at first it hung, like it did for you.  I think this is because it
>> wasn't installed by the installer.  Here is how I got around the issue:
>>
>> 1. Open cmd prompt
>>
>> 2.  Copy entire updatePaths.pl commandline generated by Petunia
>> updatePaths page to the command line and run it.  Windows should ask you
>> for permission to run perl interpreter on this file, allow it!
>>
>> 3.  updatePaths.pl should now run to completion and you should be able to
>> use Petunia to run it also
>>
>> This worked for me, let me know if it does or doesn't work for you.
>>
>> Thanks!
>> -David
>>
>> On Tue, Mar 9, 2021 at 9:33 PM David Shteynberg <
>> david.shteynb...@isbscience.org> wrote:
>>
>>> It should only take a few minutes to run the code.  Perhaps there is a
>>> permissions issue to execute that file on your computer.   Normally the
>>> installer makes sure the permissions are setup correctly.   Can you check
>>> the permissions for this file under properties -> security?
>>>
>>> On Tue, Mar 9, 2021, 8:47 PM Panyue Chen 
>>> wrote:
>>>
>>>> Hi David,
>>>>
>>>> Thanks for your fast reply and your help!
>>>>
>>>> I downloaded the code you provided and replaced the old updatepaths.pl
>>>> file in the bin folder.
>>>> While I updated the paths by updatedPaths utility in the Pentunia, the
>>>> job was not finished after around 40min. How long should I expect to get
>>>> the job done? Or could it because the web fails to connect?
>>>>
>>>> For your information I posted an image of what I selected on the
>>>> updatePaths utility page and an image of the job submitted.
>>>>
>>>> Best,
>>>> Panyue
>>>> [image: Updatepaths.png][image: JobRun.png]
>>>>
>>>> On Tuesday, March 9, 2021 at 4:34:01 PM UTC-5 David Shteynberg wrote:
>>>>
>>>>> Hello Panyue,
>>>>>
>>>>> I test the updatePaths.pl and found some problems with it correcting
>>>>> paths to directories on other drives on windows.  I have committed a fix 
>>>>> to
>>>>> this script which you can download here:
>>>>> https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/perl/bin/updatepaths.pl
>>>>>
>>>>> Please replace your existing file in C:\TPP\bin (or where you
>>>>> installed the TPP) with the code at the link above.
>>>>>
>>>>> Cheers,
>>>>> -David
>>>>>
>>>>> On Tue, Mar 9, 2021 at 9:02 AM Panyue Chen 
>>>>> wrote:
>>>>>
>>>>>> Hi there,
>>>>>>
>>>>>> I was trying to follow the PTPprophet tutorial v0.4.0 to analyze a
>>>>>> subset of data from Ferries et al. (2017, JPR, 16, 3448). I have download
>>>>>> the tutorial data into the "tutorials" folder and checked all the files 
>>>>>> and
>>>>>> directories I should have.
>>>>>>  But when I ran the PTM prophet, the job ends with an error as shown
>>>>>> in the picture.
>>>>>>
>>>>>> Please let me know if I missed any thing and how should I fix the
>>>>>> error. Thanks!
>&g

Re: [spctools-discuss] job end with error when following PTMprophet tutorial

['David Shteynberg' via spctools-discuss]

Hello again,

I downloaded the code from sourceforge and replaced my version to test and
at first it hung, like it did for you.  I think this is because it wasn't
installed by the installer.  Here is how I got around the issue:

1. Open cmd prompt

2.  Copy entire updatePaths.pl commandline generated by Petunia updatePaths
page to the command line and run it.  Windows should ask you for permission
to run perl interpreter on this file, allow it!

3.  updatePaths.pl should now run to completion and you should be able to
use Petunia to run it also

This worked for me, let me know if it does or doesn't work for you.

Thanks!
-David

On Tue, Mar 9, 2021 at 9:33 PM David Shteynberg <
david.shteynb...@isbscience.org> wrote:

> It should only take a few minutes to run the code.  Perhaps there is a
> permissions issue to execute that file on your computer.   Normally the
> installer makes sure the permissions are setup correctly.   Can you check
> the permissions for this file under properties -> security?
>
> On Tue, Mar 9, 2021, 8:47 PM Panyue Chen 
> wrote:
>
>> Hi David,
>>
>> Thanks for your fast reply and your help!
>>
>> I downloaded the code you provided and replaced the old updatepaths.pl
>> file in the bin folder.
>> While I updated the paths by updatedPaths utility in the Pentunia, the
>> job was not finished after around 40min. How long should I expect to get
>> the job done? Or could it because the web fails to connect?
>>
>> For your information I posted an image of what I selected on the
>> updatePaths utility page and an image of the job submitted.
>>
>> Best,
>> Panyue
>> [image: Updatepaths.png][image: JobRun.png]
>>
>> On Tuesday, March 9, 2021 at 4:34:01 PM UTC-5 David Shteynberg wrote:
>>
>>> Hello Panyue,
>>>
>>> I test the updatePaths.pl and found some problems with it correcting
>>> paths to directories on other drives on windows.  I have committed a fix to
>>> this script which you can download here:
>>> https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/perl/bin/updatepaths.pl
>>>
>>> Please replace your existing file in C:\TPP\bin (or where you installed
>>> the TPP) with the code at the link above.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Tue, Mar 9, 2021 at 9:02 AM Panyue Chen 
>>> wrote:
>>>
>>>> Hi there,
>>>>
>>>> I was trying to follow the PTPprophet tutorial v0.4.0 to analyze a
>>>> subset of data from Ferries et al. (2017, JPR, 16, 3448). I have download
>>>> the tutorial data into the "tutorials" folder and checked all the files and
>>>> directories I should have.
>>>>  But when I ran the PTM prophet, the job ends with an error as shown in
>>>> the picture.
>>>>
>>>> Please let me know if I missed any thing and how should I fix the
>>>> error. Thanks!
>>>>
>>>> --
>>>>
>>>> Panyue Chen
>>>> Graduate student
>>>> Dr. Hazbun group
>>>> Purdue University
>>>> [image: error.png]
>>>>
>>>> --
>>>>
>>> You received this message because you are subscribed to the Google
>>>> Groups "spctools-discuss" group.
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>>>> an email to spctools-discu...@googlegroups.com.
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>>>> https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>> --
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>> .
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Re: [spctools-discuss] job end with error when following PTMprophet tutorial

['David Shteynberg' via spctools-discuss]

It should only take a few minutes to run the code.  Perhaps there is a
permissions issue to execute that file on your computer.   Normally the
installer makes sure the permissions are setup correctly.   Can you check
the permissions for this file under properties -> security?

On Tue, Mar 9, 2021, 8:47 PM Panyue Chen  wrote:

> Hi David,
>
> Thanks for your fast reply and your help!
>
> I downloaded the code you provided and replaced the old updatepaths.pl
> file in the bin folder.
> While I updated the paths by updatedPaths utility in the Pentunia, the job
> was not finished after around 40min. How long should I expect to get the
> job done? Or could it because the web fails to connect?
>
> For your information I posted an image of what I selected on the
> updatePaths utility page and an image of the job submitted.
>
> Best,
> Panyue
> [image: Updatepaths.png][image: JobRun.png]
>
> On Tuesday, March 9, 2021 at 4:34:01 PM UTC-5 David Shteynberg wrote:
>
>> Hello Panyue,
>>
>> I test the updatePaths.pl and found some problems with it correcting
>> paths to directories on other drives on windows.  I have committed a fix to
>> this script which you can download here:
>> https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/perl/bin/updatepaths.pl
>>
>> Please replace your existing file in C:\TPP\bin (or where you installed
>> the TPP) with the code at the link above.
>>
>> Cheers,
>> -David
>>
>> On Tue, Mar 9, 2021 at 9:02 AM Panyue Chen  wrote:
>>
>>> Hi there,
>>>
>>> I was trying to follow the PTPprophet tutorial v0.4.0 to analyze a
>>> subset of data from Ferries et al. (2017, JPR, 16, 3448). I have download
>>> the tutorial data into the "tutorials" folder and checked all the files and
>>> directories I should have.
>>>  But when I ran the PTM prophet, the job ends with an error as shown in
>>> the picture.
>>>
>>> Please let me know if I missed any thing and how should I fix the error.
>>> Thanks!
>>>
>>> --
>>>
>>> Panyue Chen
>>> Graduate student
>>> Dr. Hazbun group
>>> Purdue University
>>> [image: error.png]
>>>
>>> --
>>>
>> You received this message because you are subscribed to the Google Groups
>>> "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com
>>> <https://groups.google.com/d/msgid/spctools-discuss/5f678d66-9627-4064-9467-471d489eddd5n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
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> .
>

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